Having piloted quite a bit of mech-like fighters while working on Diable, I don't think this whole "fighter" collision class mechanic is necessary or desirable. It will indeed cause some issues with some modded content, but more importantly it's way too exploitable by a player: You can sit above an enemy ship between it's guns unharmed, looking at enemy ships shooting each other to kill your fighter, and only vulnerable to missiles... So overall I don't think those ships should be fighters but regular super-frigate. I would work just as well, at least for a first release, and would soothe most people concerns.
(Quick note on the wanzers sprites: most of them were made by FlashFrozen, with some touch-up by me when I started animating them. So while I appreciate the compliment, I'm not the one the it should be addressed to)