This point is best illustrated by one of the amendments that Madison proposed in his initial speech:
"Fifthly, That in article 1st, section 10, between clauses 1 and 2, be inserted this clause, to wit: No State shall violate the equal rights of conscience, or the freedom of the press, or the trial by jury in criminal cases."
This clause, seemingly innocuous to us today, was rejected by the Senate in its final draft of the Bill, and the concept that any part of the Bill of Rights would apply to the states was still 100 years away. Several cases that came before the Supreme Court in the 19th century attempted to have the Court establish that the Bill should apply to the states, to no avail:
So Madison had wanted to place limits on state powers in the BOR, but Congress did not include that language.
That is just silly. Using your logic, they should never have included Art 6 para 2 then. Nor should they have included Amend 10.
That didn't mean they didn't want the Rights of the People to be recognized by the states.
States wanted to keep their own authority regarding religion and other such matters. Thus, the scope of the First Amendment is limitted to Congress. You suggest that the authors and ratifiers deliberately wanted the First Amendment to apply only to Congress rather than to the states, and wrote the language to make that clear. If they likewise wanted to make the Second applicable only to Congress, is there any reason to believe they would not likewise have made that clear?