Hi all! Thanks for your input in this matter.
For now, I have solved my problem by creating the needed resource files from my own code, before I register the plugin using these newly created resource files. This will do for now, although it means I have to ensure that the "res" folder of my plugin has write permission. I will try to solve that in the installer.
"What might be the confusion here is, that you can of course register the same implementation multiple times. But these then would pop up as different plugins in Cinema 4D - which is probably not what @Filip is trying to do. At least from my current understanding."
-This is actually exactly what I am doing! I am registering the same plugin class multiple times, using a different ID. Since the behaviour of the class depends on the ID, this appears to the user to be a series of entirely different shader plugins, which is my intention. The problem was that each such plugin also needed its own unique resource files (to avoid the problem that the resource name has to be unique). But as stated above, I'm solving this by creating the resource files themselves on the fly, whenever they are needed.
I consider this problem solved for now.