Wonder Boy in Monster Land is one of the few SMS games that don't work with the Genesis controller. This is true whether you're using the Power Base Converter or a flash cart. I play on a Genesis with an Everdrive Pro, so this prevents me from playing the game. I could of course plug in an SMS controller, but given that the D-pad on those things were made by Lucifer himself, I'd rather not.

There is an IPS patch that fixes the game and makes it work on a Genesis controller. Would it be allowed to use this patch and submit runs or am I going to have to bust out BizHawk?

This website explains the fix.

https://krikzz.com/forum/index.php?topic=1203.0

I believe these games don't work due to the Japanese/Export check the games perform. Part of the region check toggles the select line on the controller port. It's supposed to be reset but these games fail to do that.

I patched the games to reset the select line or bypass the part of the region detection code that writes to the select line.