I've just beat the extend mini campaign today and wonder if I chose the bad ending in vanilla, would it change the ending slide since several teammates would be unavailable?

AFAIK, you can, leading to some unexpected results. If you accepted Xian Ya's offer of 10 years of good fortune, some very improbable things are supposed to happen that will benefit you.

I haven't tried this myself, yet, though. I'm a little hesitant, because I'd have to kill several of my party members, leaving only Gaichu and Racter. And whatever runner you hire to fill the gaps in your team.

Yeah, that sounds somewhat intriguing but didn't choose that end the first time around.
I hope if we choose the "evil route," we at least get extra "fortune" for sacrificing that many companions. That run would also require specific build since Gaichu without aim spell buff cannot hit a thing in the later missions...