Some zips work perfectly, others have to be disk swapped, and some don't work at all.

So just stick to WHD load .lha games that contain the full set of disk files.

I ended up setting up a cron job and got this working.

@Darksavior check the instructions made by joolswills in the comments here:
https://github.com/RetroPie/RetroPie-Setup/pull/1602

Maybe it get some improvements in the future, but you can change it currently.

@denisuu Hi i have the same problem i wanna how you do for fix it?

It doesn't seem like this is possible due to my SPI screen and GPIO SNES controllers both needing the clock pin on the Pi, plus the scripts don't seem to be easily configurable, so I decided to order a USB SNES adapter. Hopefully I didn't fry my controller when I was trying to hook things up concurrently today.