From the sound of things with the patch, new Form and Ref Objects are being added to the ESM. Last time this happened, there were more than a few FormID Mixups.
Those who know what they're doing with FNVEdit can use that app to find any errors with improper FormIDs.
I don't believe so. That being said, fo3 had other serious problems with patches. The whole converting all esps to esms using master-override was spawned from a lousy fo3 patch.