Yeah, sadly there's a lot of hard-coded stuff. I'd really like to change the warp effect or the default fighter commands, for example, but that's just not possible without ugly and error-prone workarounds.
As for fighters jumping in on their own, could you perhaps make an invisible object that's completely undetectable to launch them from?
If that undetectable part can't be done, you could call it a subspace disturbance or something instead I guess.
Should be easily possible, although that invisible object would at least appear on the target list. Not really a big deal, though.
Now onto some new images
Aeolus and fighters heading into battle:
Two Aeolus cruisers approaching each other firing blobs, flak and aaa beams:
Lovely beam cannons...
The new fighter warp-in effect: