Hi!
Bug: AFR grows 100x for 10x increase in ship size. For a quick test create a new ship, slap a 1HS engine on, and keep adding armor. At 500t AFR is 2%, at 5000t 200% and at 50000t 20000%.
Also, at high tonnage, removing the engineering bay dramatically reduces the AFR, replacing it with a smaller one, especially the fighter version, makes the AFR become even more ridiculous.
Apart from that, computing the AFR just on the size of the ship is a bit too simplistic in my opinion, at least for a game like this. It means some huge carrier with some low power engines and otherwise pretty much just hangar and armor will have a very high AFR, while a small ship crammed full with high power components will have a low AFR. Or just replacing a big, low power engine with small, high power one will also decrease your AFR. But of course, that's just a minor gripe, keep doing what your doing!