It is true that even the pure vanilla section of Purr Data is not 100% the same or compatible. I already mentioned how Purr Data doesn't carry yet all of the features from the latest Pd Vanilla (0.48) - though I know it'll get there eventually. Some of these considerations we're bringing here have to do with the Purr Data project being still relatively new. I'm expecting it to be more fully compatible.
But besides Purr Data not integrating all of vanilla yet, it also has some different functionalities of Vanilla's objects. Even regarding syntax, like being able to load $0 in messages (and boy, do I wish that was in Vanilla). So that can be tricky as well.
Anyway, I don't think is that bad to go ahead and use both ;)
cheers