FWIW, I did manage to get this working. For future people with similar issues, I ended up getting desperate and plugged my config and logs into ChatGPT and it figured out the issue - misplaced quotation marks.
This was the config that worked for me:
executable $HOME/Desktop/emulators/retroarch.app/Contents/MacOS/Retroarch
args -v --fullscreen -L "$HOME/Library/Application Support/RetroArch/cores/snes9x_libretro.dylib" "[romfilename]"
rompath $HOME/Desktop/ROMcollections/TOP100SNESGAMES/
romext .sfc
system Super Nintendo (SNES)
....only differences was found in the quotation marks. After that I had a problem with the Retroarch screen losing focus which was then solved with the "--fullscreen" addition to my arguments. Running beautifully now!