Nonsense. Congress has the power to alter in-court procedures by passing a law and has done so many times. Here's just one example. Here is a public law passed by Congress and entered into the U.S. Code that modifies the Federal Rules of Civil Procedure in regard to jury selection. First the law:
28 U.S.C. 1870.Now the relevant part of the Federal Rules of Civil Procedure as it appears in Chapter VI, Rule 47(b).In civil cases, each party shall be entitled to three peremptory challenges. Several defendants or several plaintiffs may be considered as a single party for the purposes of making challenges, or the court may allow additional peremptory challenges and permit them to be exercised separately or jointly.
http://www.law.cornell.edu/rules/frcp/Rule47.htmRule 47. Selection of Jurors
(a) Examination of Jurors
The court may permit the parties or their attorneys to conduct the examination of prospective jurors or may itself conduct the examination. In the latter event, the court shall permit the parties or their attorneys to supplement the examination by such further inquiry as it deems proper or shall itself submit to the prospective jurors such additional questions of the parties or their attorneys as it deems proper.(b) Peremptory Challenges.
The court shall allow the number of peremptory challenges provided by 28 U.S.C. 1870.(c) Excuse.
The court may for good cause excuse a juror from service during trial or deliberation.
If the Act only provided for jurisdiction consistent with Article III and 28 U.S.C. § 1331, the Act would not be in violation of the principles of separation of powers. The Act, however, goes further. Section 2 of the Act provides that the district court: (1) shall engage in “de novo” review of Mrs. Schiavo’s constitutional and federal claims; (2) shall not consider whether these claims were previously “raised, considered, or decided in State court proceedings”; (3) shall not engage in “abstention in favor of State court proceedings”; and (4) shall not decide the case on the basis of “whether remedies available in the State courts have been exhausted.” Pub. L. 109-3, § 2. Because these provisions constitute legislative dictation of how a federal court should exercise its judicial functions (known as a “rule of decision”), the Act invades the province of the judiciary and violates the separation of powers principle...
There's more detail, but this is the gist of it. In other words, Congress did everything it could think of to predetermine the outcome of the case without actually stating so. And, yes, that is unconstitutional.