I think the piece that's missing in your assessment is the timing of the agreements. For the vast majority of students, these NIL agreements won't be signed until after they have signed on with the school, even if they are negotiated (and maybe even reported) beforehand. The prohibition the NCAA thinks that it can enforce is for an NIL agreement as an inducement to attend a specific school ("pay to play"). So if I sign a student to a NIL deal that says "we'll pay you $10,000 to sign with the University of Minnesota," that would violate the NCAA guidance. But most NIL agreements won't be signed until after the student commits and are, in theory, therefore not an inducement to sign with a school because the student has already committed to the school before signing the NIL agreement. Of course that will often prove to be an artificial distinction as you suggest.
But the agreements themselves can be linked to athletic participation at a particular school. Example, if I own a restaurant in Maple Grove and sign a NIL deal with a Gopher student-athlete, that agreement can be limited to the time he or she is participating in a sport at the U. Payment can terminate if my endorser transfers, quits, gets expelled, etc., so the agreement is specifically and expressly associated with the school.
The Arch Mannings and Zion Willaimsons of the world who have significant marketability regardless of where they attend school are pretty rare. Most students will have to sign with a school before they can sign their NIL deals.