Do you have a rom or source code that you can post? My guess is that with Mesen-S it's initializing VRAM to a randomized state (instead of all zeros). Typically that's a emulator config option which would explain the discrepancy between different emulators. Are you using $212C to disable layers you don't need? You can also go into the debugger of bsnes or mesen-s to look at what's in VRAM.
As for tutorials, the ones on the SFC wiki are pretty good, I've followed a couple. libSFX also has a good set of sample programs, but they of course take full advantage of libSFX macros so it might not be an option if you don't want to do that. Unfortunately the issue with homebrew is many people develop tutorials and sample programs based off of aging and inaccurate emulators. For example the hello-snes repo you linked doesn't work on actual hardware either, and it seems like it was developed using snes9x (considered to be out of date at this point)
I've just created a small section in the main jam page with spots for folks to ask for help if they get stuck. There are others that have way better knowledge of the hardware than I do