Aloha,
Unless it's a documentary, NO movie is within the continuity of the book it's based upon. However, the original idea of the Countdown was to highlight the Amazing Spider-Man(the foundation of the character) in relation to the movies. All three movies took elements from Amazing Spider-Man and related IN CONTINUITY comics. Not going to go on an ANTI Ultimate rant (I'll save that honor for TMOB

), as much as to say that the movies SO FAR- are based upon Amazing Spider-Man and not an alternate universe Spider-Man. But, if you want to start a countdown using all Alternate Spider-Man books(Ultimate,Spider-Man 2099,Unlimited v.2)-Go For It!
Spidey rules