As I recall, there were 2 versions of the Game Express Card - version 1.0 and 1.1 .
I don't recall if one of them (1.1) relied on the built-in memory of the Duo, but I believe that the original one did not (and games could only use the 64KB of RAM on the original system).
Games written for v1.0 could be used on v1.1, but not vice-versa. I don't recall which games were associated with which, but I'm pretty sure there's a list somewhere on the internet.
The cards implemented ISO-9660 filesystems, so those games can more easily be read by computer. Aside from the previously-mentioned copyright angle against using the original CDROM card, the ISO-9660 filesystem could have allowed them to have faster test-cycle times - since SCSI buses allow multiple hosts on the same bus, the CDROM on a PC-Engine setup could have been replaced by a PC hard drvie, which could also have been updated in real time by a PC, for fixes to graphics, sound, programming, etc.