While you are correct that the Prequel comics for both the first and second movies are not recognized by Bay as canon…I seem to remember one of the screen writers (I believe Orci) believing (key here is believing) that they were canon.
As far as Bay is concerned whatever he believes to be canon and not is not my concern. The man wouldn't known Fortress Maximus from a stump in the ground.
But thats just me
I am gonna have to go searching for these interviews….again (*_*)
Anyway, the Prime killing a Prime may have been answered in one of the Junior Novels.
Personally I want to see a Battle Between Superion and Bruticus
::edit::
I purchased a similiar book with technical data for the Transformers from a Barnes and Noble the day the movie came out…I wonder if it was the same one…What was the name of it?