Umm, the idea that JME's limitation is based on when the genetics of the user existed is completely baseless and pulled out of your imagination only because it supports R=U. Nothing in the game supports it so it doesn't count in any way as a supporting fact for R=U.

The game on the other hand makes it quite clear that Ultimecia lives many generations into the future where none of the main characters could technically exist (i.e. they should be dead by then). Even the most feeble interpretation of "many" still leaves Ultimecia hundreds of years into the future. The only way to make R=U work is to suppose that Rinoa somehow found a time machine and used it to get to the future, which is of course not supported by the game at all.

R=U only works if you imagine it is so. In reality, the game doesn't allow it.