Actually most of Whedon's alien four script was completely reworked. That said, hey, fellows who think this is the same universe as the Fantastic Four and X-Men movies? It's not. It's a completely different Marvel universe, just as this is not the same Universe as the standard Marvel Universe, nor is it the Ultimate Marvel Universe.
So no, it won't be confusing, because no one watched Fantastic four, as it sucked. Oh so bad.
Whedon's a great writer and director, and also writes wonderful comics (please see Astonishing X-Men).