wait, somewhere I'm lost....
Lets take factory setups out of it at least for now to help my feeble mind.
The aftermarktet unit is spliced in and if I'm not mistaken doesn't use the factory code at all. Its spliced into all the power wires for the door lock, starter, sunroof, whatever you have it hooked into.
Then it uses its own code to control these functions making the old fob worthless as the new one is doing its job on its own without using any of its code (so perhaps that one still works as well? never tried it) going to its own receiver installed in the car.
Assuming I'm right so far, why again can't there be an app that is set to send this code to this receiver?
Sorry if this is making you talk in a circle, I'm just trying to fully understand.