> gameboy games would be a trademark violation because of the security involving the nintendo logo being rendered on the screen by the cartridge and then being compared to one from ROM

This is legal. It's analogous to the TMSS mechanism used by Sega in the Genesis; Sega v. Accolade [1] established that a "trademark violation" which the trademark holder forces to occur through technical measures is not, in fact, a violation.

[1]: https://en.wikipedia.org/wiki/Sega_v._Accolade