I read an article at the time where Ring explained why Margarito & Mosley wasn't a championship fight.

If I recall correctly they asked the expert panel that decides these things (it's like a hundred journlists and fight industry people -there is a list of these people online somewhere too, I know Barry McGuigan is one of them) and they decided, and I think it was quite tight too (maybe even 51%-49%), against declaring it a Ring Championship fight due to Mosley's loss to Cotto.

At the time I thought that had Margarito won it was a little tough on him that he wouldn't be named champion, but as Mosley won and was ranked below Cotto (and having lost to him previously) it was the correct decision.