I highly doubt whether that had any bearing tbh. He was gainfully employed by Hollywood during that period, being given huge projects by Fox and Warners before and after. He was working closely with Star Trek's biggest star as well as a host of other A-listers. The Weinsteins were at their zenith.I assume Berman heard enough of all the BTS issues with Singer that he was like “nah, we’ll give you a one second cameo, but nothing more”.
It's more likely that he wasn't gettable by Paramount at that point because of his work on X2 when Nemesis was in production.