Basically, they didn't.
I have, and still use, a Roland LAPC-I card. This is used as a midi interface for an old computer, but I do also use the sounds on the card, and I have a number of rather pleasing midi files that are set for the MT-32 sound set, and not GM. The percussion sounds are assigned differently from GM, maybe not ALL, but at least some, so if I play a GM midi file via the Roland card, it just does not sound right. I can load a GM patch set for the main instruments, but this does NOT change the percussion assignments.
Any software that I might be working through would need to know that the sounds were, both the normal sounds, and the percussion. Normally, I'd just select the instruments manually. Some older software might have a MT-32 setup, then the MT-32 instruments were fairly common back then. The Proteus device you mention would prob need it's own 'map', and this was maybe not as common.
Normally, percussion is selected via a single PC (Program Change), and different instruments are then selected via a note number (key pressed). This means that you NEED a channel available to use for percussion. You cannot mix pitched notes and non-pitched percussion on the same channel without causing a sonic mess. So only ONE 'sound' (either percussion set, or tuned instrument, would be active at any one time on a channel. If your Proteus had a way of doing something else, then this was peculiar to the Proteus.
Geoff