So again, I will ask you. Did you read the posts?
Of course I did, you've made quite a name for yourself in the PiStorm community with this, I'd literally forgotten I had an account here now!
I have to say though opening up your Amiga to remove the SD card so you can go back to stock is quite the bold move.
Edit: I am reminded that there is indeed a stealth mode for the PiStorm that would serve much better than trying to run the accelerator without an Emu68/FAT32 partition present - the long press on the ol' three-finger death grip will disable the PiStorm temporarily until the next power-cycle. That would get floppy-only games into much better shape compatibility-wise, but you would indeed lose the benefits of FastRAM and a quick 68k CPU.
All in all, it is probably easier to run the game through WHDLoad, assuming a slave exists.