Not in any practical way I can think of. Game Genie can only replace values in cartridge ROM, and booting from the cartridge slot at all rearranges the Genesis/MD memory map compared to booting the SCD/MCD BIOS, so I don't see how you could get the AR software loaded and still boot CD games.
If not how hard would it be to code simple trainers that you could patch the isos with?
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