Patrick, unfortunately I am not the right person to answer your question. The 1st gen Magnic Lights I have are more similar to the current "Wega" line than "Micro" line, in that it is not associated with the brakes at all, except to use the cantilever brake stud as a mounting point. You can see that from this
pic from the review I've cited; the light attaches to a bracket that's bolted to the cantilever boss/stud.
If you're adding a Magnic Light to a disc brake bike, you should more properly select the "Wega" line. Those clamp onto seat stays or fork blades, and are completely independent of any brake type.
Finally, I would be surprised if the rim brake pads are proprietary. It appears that the proprietary part is the brake pad holder. Even if the holders are a bit odd shaped, I'm sure one can modify generic brake pads to fit, because cutting/trimming pads shouldn't be difficult, especially if one has a Dremel tool.
Good luck!