Are any of them allowed for runs? Hard GPU sync, frame delay, run-ahead, etc.

I'm not the most knowledgeable about Retroarch so I'm not sure what most of these do but I imagine that at the very least frame delay probably works the exact same way as Mega SG's zero delay (changes fps from 59.9228 to 60 to account for any frame delay in inputs).

I can ask Zaxon or Joeybaby what settings they use in some of their runs, but the safe bet would be to stick with the default settings since that is arguably the most accurate to console judging by the discussions that took place with the Ducktales 2 community