Not a complaint, just an observation and a heads up to anyone else that wants to do this.
In the SNES9x core (what you want to use for multitap SNES games), you have to change player 2 to the multitap, and then save a core or game override. The specific override is: input_libretro_device_p2 = “257”
However, in Genesis Plus GX (what you want to use for Genesis multitap games), you have to change player two to ‘Team Player’’ or '4 way play, ’ and then save a core or game remap.
It’s a little confusing that these two cores don’t work the same way, but for someone who wants to auto configure all of their Genesis/SNES multiplayer games, this is how you do it.
Edit: Looks like I might be mistaken on this - in Genesis Plus GX, either method will work, but if you have a core or game remap, it will override a core override. That might actually be the reason I was having problems with SNES9x too.