You have misunderstood the holding in Ryder.
The key passage from Ryder: "Unlike the defendants in Ball, McDowell, and Ward, petitioner raised his objection to the judges' titles before those very judges and prior to their action on his case. And his claim is based on the Appointments Clause of Article II of the Constitution--a claim that there has been a "trespass upon the executive power of appointment," McDowell, supra, at 598, rather than a misapplication of a statute providing for the assignment of already appointed judges to serve in other districts.
So we see two grounds upon which the Court relied upon for not applying the de facto officer doctrine:
(1) He raised his objection to the qualification of the judges in the legal proceedings prior to their ruling. Of course it would have been nonsense to ignore his legal challenge to the judges' right to sit and then after the judges rule, claim that it is "too late, their decision is now protected by the de facto officer doctrine." He raised his objection in a timely manner BEFORE the ruling. The de facto officer therefore should NOT apply in those circumstances. The Court got it right.
(2) The case was not merely a question of whether an officer (judges in this case) failed to meet a specified eligibility criteria (such as age or residency). It was whether the manner of appointing the court itself complied with the Constitution.
The facts in Obama have nothing in common with Ryder. There is no analogous claim as in Ryder that the composition of the office of the presidency itself violates the Constitution; indeed, one can't make that claim, because the office of the president is established directly in the Constitution itself.
And because of standing issues, the Courts have refused to entertain claims on the merits that Obama is ineligible, unlike in Ryder. It would be analagous to Ryder if a petitioner were to challenge a pending but not completed executive action by Obama that affected him and after his challenge was raised but before the final resolution on the merits of Obama's eligibility the executive action was taken, following which a decision on the merits as to ineligibility is made by the court; clearly, the de facto office doctrine, as in Ryder, does not support giving effect to that executive action.
Obama's case, on the other hand, is a straightforward application of the de facto officer doctrine. The law requires that to be eligible to the office he be 35 years old, lived in the U.S. for 14 years and be a natural born citizen. If, unknown to the citizenry at large and the Congress, at the time of qualification the person holding the office did not meet one of the qualifications for office, then the facts would be a textbook case of the de facto officer doctrine.
To argue that the De Facto Officer Doctrine would apply even when it explicitly violates the Constitution is to essentially argue that the constitution is meaningless and unenforceable. Such a doctrine would also logically suggest that the constitution is not in fact the Supreme law of the land, since it can be disregarded with impunity by the government--which would also ironically be a violation of the Constitution's Supremacy Clause.
Applying the DFOD in the face of a direct constitutional violation would absolutely subvert the law in the name of maintaining order. It would also encourage the violation of the law since those impersonating an officer under the color of law would be able to get away with their acts being upheld even if they explicitly violate the constitution. This doctrine would ultimately subvert the rule of law in the name of saving it. It's a choice between sacrificing law and principle (the constitution) at the expense of order and convenience, or choosing temporary order and convenience at the expense of law and principle . Take your pick.
The de facto officer doctrine in no way violates the Constitution.
Let's go back to first principles:
In my view, I believe the courts would hold that the power to determine whether the person chosen for president has qualified for the office is exclusively given to the joint session of Congress at the time of the counting of the votes, and that the Constitution does not permit the courts to usurp that function by second-guessing the determination of that joint session of Congress that the person chosen is either eligible or ineligible.
Therefore, the ONLY method for removing a president where there appears later evidence that the president was not in fact eligible is through an impeachment/removal proceeding in the House and Senate.
The legal nature of this proceeding is NOT to overturn the finding by the original joint session of eligibility; the Constitution does not contemplate re-opening the joint session of the counting of the votes AFTER the person has been found qualified and installed. Rather, it would be removing the president for a high crime and misdemeanor in the nature of fraud for deceiving as to his qualifications.
So as a technical matter, by impeaching and removing him the House and Senate do not legally rescind the original finding of the joint session that the president was eligible. Rather, they find him guilty of a high crime and misdemeanor and remove him with effect from that point on. The actions taken by the president prior to his removal would continue to have legal effect.
The De Facto Officer Doctrine is a specific manifestation of a more general principle: not every wrong has a remedy. I think those applying such a principle, however, misapply another important principle: the fact that there is no remedy for an illegitimate action does not make the action legitimate. I would suggest that the DFOD should not be taken to say that the actions of the DFO are in fact legitimate, but rather serves to limit the remedies which would otherwise be available on account of its illegitimacy.
I think the failure to recognize the distinction between the legitimacy of an action, and the availability of a remedy, is behind much of the horrid court precedent that plagues this country. Essentially, the Court takes the position that because prior decisions generally have to be acknowledged as legitimate, the Court must act as though the Constitution and laws have enough nooks and crannies to justify them. The net effect is that the Court makes decisions not based upon the Constitution the Founders wrote, but rather based upon an amorphous fantasy version which continuously adapts itself to fit every decision the Court hands down.
The Constitution is a relatively simple document. If the Court were to recognize that it is neither necessary nor proper to maintain the fiction that every Court decision is legitimately decided, the comparative simplicity of the Constitution would again be revealed. Among other things, when the Bill of Rights uses terms like "unreasonable" or "excessive", such terms are not supposed to be defined primarily in terms of judicial decisions which have held that certain things were appropriate and certain things were not. Rather, they should be applied at face value: if a jury which has examined all the facts surrounding a case would regard a particular punishment as excessive, it is. If a jury which has examined the circumstances surrounding a search would find that it was conducted in unreasonable fashion, or the cop who sought the warrant did not have bona fide probable cause, it should regard the search as illegitimate and not construe against the person who was searched any evidence gained thereby.
If a defendant asks a judge to examine the conduct of an officer in a search, and the judge determines that there is no way an impartial jury would regard the search as "reasonable", it may be appropriate for the judge to suppress the evidence on the grounds that jurors may find it hard to let a guilty person go free if the evidence against him, though illegitimately gathered, appears genuine. On the other hand, it is neither fair nor proper for courts to declare that the the question of whether a search was conducted in "reasonable" fashion should be regarded as having been "settled law" even before the search has took place.
Returning to the DFOD, the right and proper thing for the Court to do would be to acknowledge that the gross misdeeds of various people [including alas many justices themselves] had created a situation where the government has performed many illegitimate actions; allowing such actions to stand would cause unjust harm to some people, but rescinding such actions would cause unjust harm to others. The DFOD is meant to protect the interests of those who would be unjustly harmed by rescinding an apparently-legitimate action should be given priority over those who would be harmed by upholding it. It is not meant to protect the unjust enrichment of those who would benefit from the illegitimate action. The proper resolution is to roll things back in a manner such that (1) those who had a good-faith reliance on the legitimacy of the actions end up about as well off as they would have been without such reliance, and (2) those who would be harmed by the actions are not harmed any more than necessary to achieve (1).
One major problem with trying to apply the DFOD to the present situation is that in general it is designed to ensure that companies have no incentive to leave a phony officer in place. Applying it to the present situation, however, would have the opposite effect. The people who are sheltering the phony officer would be the ones hoping to benefit from his actions; letting them get away with it would encourage more such malfeasance.