I disagree that an Act ever has legal relevance to an Amendment, particularly if in more recent cases the amendment was invoked.
But the 14th amendment specifically gives Congress the power to enforce it in two places:
In Section 3:
But Congress may by a vote of two-thirds of each House, remove such disability.In Section 5:
The Congress shall have power to enforce, by appropriate legislation, the provisions of this article.How does Congress enforce a Constitutional provision except via acts?
The Amnesty Act of 1872 removed the disability just as Section 3 said Congress can do. The question is whether it removed it only for people who met the conditions at the time or if it removed the disability in perpetuity because it wasn't specific except to excepting two Congresses from it.
-PJ