Could be either all other things being equal, but in the "mapping of old Rome params" at the end of the file, which is the template for the new AI, there are also a bunch of these "SPECIAL CASE EXISTS HERE IN CODE FOR SUCH AND SUCH" comments. There's one in the beginning in particular, saying "special case here for not allowing attack of trusted allies". In the code used by the game, the comment does not appear, and in it's place ... is a condition (not appearing in the old code) forcing the AI not to attack its trusted allies.

Which is what leads me to believe that all those special cases comments are just that : a "blueprint" for what could/should be done and where to put it so that it works, and not an explanation of what happens elsewhere (after all, I'd assume CA people working on the files would already know, or would easily find out what happens elsewhere, even though my work on the traits left me with some doubts regarding this :) ).