Yeah, but that was after his contract had expired and he'd become a free agent. As far as I'm aware, the rule applies to new players rather than contract extensions. After that, the amount becomes irrelevant, he could accept a wage of £1 and they still wouldn't be able to register him because he would be considered a new player when they were already over the cap.
I'm saying why didn't they try to extend his contract much earlier, once Bartomeu was gone which seemed to be the crux of Messi's issues last year, and Laporta was in, you'd think that was the time to try to do it rather than let it lapse and complicate matters as it did. Pique, de Jong, Lenglet, and Ter Stegen all signed new deals in October, they hardly seem like pressing issues by comparison, and was one of the last acts by Bartomeu.