I have used a Software Modded NES Classic to do runs for KI, and I'm just wondering if I can use that same hardware for my runs. I know it says in the rules that the emulations HAVE to have the full window to see if it's the right version, but I'm curious if I could use the same hardware for the MK runs as well.

You only need to show the window for the categories of emulators as they have tools that help to have some advantage in racing and for original hardware is not necessary, enter the community Discord and call the moderators that they will answer your questions.