I need to test it (never actually played with BG), but if they're implemented using anything other than the stock ModuleEngine, then no, TCA won't even see them as engines. That's exactly what happens - TCA does not recognize the engines. Are there any propeller/rotor mods known to be working with TCA? I didn't find any info on this but for the mention of propellers in the first post here.
TCA is really useful for all kinds of fancy aircrafts with jet engines! However, I didn't manage to make it work with rotors + propellers or heli blades from Breaking Ground. Is this a known issue of I'm doing something wrong? Could not find discussions of any issues about this.