Okay, that’s plausible. It probably doesn’t fit Occam’s Razor, but it IS plausible.
Plausible doesn’t get us very far, though. It’s plausible that the Director of Hawaii’s Department of Health conspired with the Obama administration to produce a totally fake birth certificate. But I know of no one who has any actual PROOF to that effect.
Suppose Mr. X is dead. Mr. Y was known to dislike him. Mr. Y was in the same city that night. But there’s no DNA evidence, no witnesses, no proof of any kind. It’s plausible that Mr. Y killed Mr. X, but we can’t convict and hang Mr. Y without some actual convincing PROOF.
In fact, when it comes to the layers, it would’ve been a lot easier for them to just produce a fake certificate and scan a flat image than it would have for them to go to the lengths you describe. So that leaves the scenario you describe probably quite unlikely. If they were going to fake it, why not hide the changes in a flat image? Far, far easier, and fewer questions asked.
Were I a tinfoil hatter, I would suggest that this was done because they put their finger to the wind and decided most of the electorate was "anti-birther". So what more strategic move than to finally release the long-awaited BC with (oopsy!!) hidden flaws, thus portraying those who find those flaws as hair-splitting extremists with nothing better to do...while "sensible" people see the whole issue as "settled" and the so-called birthers as even more extreme than they were before.