But the point is Marshall and others didn't feel there was a conflict. They felt 'All Judicial Power' means something and interpreted this way. I agree with Marshall and Hamilton. That's what Judicial Power is. It wasn't a big deal at the time if I'm not msitaken. The framers generally saw this to be in line with their intentions. At least if you go by the Fedaralist. Jefferson didn't like it but he was not one of the framers.
Congress specifically has the power to limit the areas over which the Supreme Court and federal courts may rule. That authority has never been used, to my knowledge, but it is there in the text of the Constitution.
And "The Federalist" is hardly the only source of illumination on the intents of the writers of the Constitution. There was this little group called "anti-Federalists" who had other ideas--said ideas which resulted in the addition of the Bill of Rights.