Cribbing a bit from how the UperGrafx appears to do it, would it be possible to do the in-game reset detection in the BIOS/System Card screens instead of attempting to steal cycles at runtime? To be clear, the user experience here would be:
1. User holds Run and presses Select.
2. The game's normal reset logic kicks in here. The SSDS3 isn't doing anything.
3. User goes back to the System Card screen.
4. IGR logic engages for the System Card and sees them continuing to hold the buttons for X frames and then jumps back to the SSDS3 menu.
What I'm not sure of is how this would work with HuCard emulation. I don't know if the standard reset logic gives the BIOS a chance to kick in, or if a HuCard reset is just a "jump to $0000."
Anyway, it's food for thought. It could potentially make IGR consistent.