Your first suggestion is quite valid, setting up custom twist bones, although I’d say unless you have fair amount of rigging experience, probably don’t do this. Either way, I’d probably not do this unless you really want a proper custom rig, it’s not really worth the effort. Biped has perfect twist bones without any weird side effects that you get by trying it yourself. Setting this up can be quite problematic.
Your second suggestion is possibly a good one. I think that’ll work pretty well. Just replace the twist bones but still drive them with Biped. Setting that up is simple. Only one concern I’d have there is that on export you’d probably still get the Biped bones in there, just because they will be part of the hierarchy, even if they do nothing. But I’m not sure if you “export selected” if that’s the case. May need to do cleanup after export using this method.