The prevailing understanding today--at least the functional one--is that the Constitution means whatever at least 5 of 9 Supreme Court justices say it means. My read of the Constitution is that it means whatever 2 of the 3 branches of the federal government say it means. A defender of the current practice can argue that the Court can assume that the executive and legislative branches are aware of their decisions, and if they disagree they have remedies to change any decisions they don't like--e.g., the legislative branch by passing a law, limiting the scope of the Supreme Court's jurisdication (a power specifically provided to Congress in the Constitution), initiating an amendment, or impeachment; the executive branch by ignoring the ruling. The legislative and executive branches are in turn held accountable to the electorate. The problem--the legislative and executive branches have failed to use these rememdies, thus granting the judicial branch with enormous extra-Constitutional authority. To take it further, the electorate has tacitly gone along with this course of appeasement.
Congress can only limit the Supreme Court through Constitutional Amendment. It's only the Appellate courts they can affect through laws.