That "Each House may determine the Rules of its Proceedings" appears in the Constitution.
Exactly. BUT....what doesn't appear is that the Senate Rules of 1890 can bind the country for the rest of history.
This Senate cannot be forbidden from establishing their own rules of the Senate in exactly the same way as the rules for their Senate were established by the very first Senate.
THAT is establishing something in history that amounts to a constitutional amendment without going through the constitutional amending process.