I have a question regarding automata theory that I think is more theoretical than simple "How do you translate this PDA to a CFG?" stuff that would obviously seem to go into Computer Science. I, however, can see a good argument that all automata theory questions should now go into Computer Science. Does automata theory still belong here at all?
Yes, automata questions are considered on topic here. Regarding whether you should ask here or on CS, I would recommend asking wherever you think the question has a better chance of getting a good answer.