Yes, the FM tweaks pack includes FM tweaks per all 11 folders for each individual aircraft tweaked (squad, quick combat, main, etc.) - so, technically, the changes are also valid for the AI-flown planes too since all the aircraft folders for each type I work on are tweaked/duplicated (the xfm files).
I've noticed this myself when going up, in a Nieup, against the tweaked Alb. D.II variant with 180 hp, for example; the AI is more capable in it than in the stock (160 hp) Alb. D.II (better climb, etc.). Another good example is the Vickers-armed Nieup.23, tweaked to become a 23bis (125hp, better top speed, climb, etc.) - it becomes a more capable opponent, and is also more capable when player-flown. The tweaks are fairly subtle but realistic - I've tried to carry over much of the "feel" of my FM tweaks for FE2 - so it doesn't break the AI or do anything silly with it.
For a fun test, load up my tweak for the 150hp Fokk. Dr. I and then go up against it for a world of hurt - I can barely knock that monster down but I have to load up something equally potent such as the engined-up Nieup 25/27 tweak I've included (165hp) with my previous FM packs, or the 220hp rare Spad 7 so I can get away from it in a hurry if necessary.
How the AI fly the tweaked types also depends on their skill level: novices and regulars might not do as well as seasoned pilots and aces. My tweaks tend to make the types a bit more slippery when landing (more float, yaw, etc.) - and I've increased fuel consumption rate on them a bit, by about 10-15%, depending on engine type.