Basically there are two things:
a) the camera has to be told that firmware (autoexec.bin) is being loaded from a bootable memory card at boot-time
b) the memory card has to be bootable for the camera to find the autoexec.bin on it
Now, with a) active, I could find no way to have the camera start-up with the Eye-fi X2 Pro card in it. I tried making the Eye-fi card bootable, non-bootable, formating it, placing and not placing the autoexec.bin on it, using it together with the CF card, using it together with a bootable CF card with autoexec.bin on the CF etc. A normal SD card works fine without issues.
Without the Bootdisk flag set in the camera (a) the Eye-fi works without any issues.