Just curious here... what kind of protection does the Atari GT hardware have that makes it so difficult to emulate? Special chips? A security scheme at the board itself? Lack of documentation?

Unknown undocumented custom ASICs that can alter the contents of RAM on their own. Basically the worst possible case.

Fixing it will require at least a logic analyzer and probably custom hardware like the guys who cracked Space Lords and the Gaelco Dallas stuff.

Thank you for the detailed explanation RB.