A few points on this:
I don't think GEM module is relevant, didn't that come in later (Mk1.5) - this seems to be an early Mk1 (like mine).
The locking system has 3 effectively independent components in each key (2 for a non-remote):
1. The blade, cut to the relevant code, enables lock barrels (including ignition) to turn.
2. The immobiliser chip, enables starting/firing of engine. With 2 valid keys/chips known to the car you can program more. With just one you need Ford or an auto security specialist to add the second.
3. The remote functions lock/unlock/boot. These are programmed separately (all together) but you do need one working key (blade, maybe immobiliser) to get the car into "remote learning" mode.

You can easily program a key to remotely lock/unlock that has the wrong (or blank) blade and no/wrong/invalid immobiliser chip. As noted above it's independent.