Are you talking more about the hardware or the software? On the hardware, I'm fine to go to the same level as Axoloti which is schematics etc but not full layouts. That's simply to prevent someone from just printing clones directly.
On the software: there's a subtle issue with how the firmware works. It depends indirectly on information derived from a proprietary manufacturer toolchain even though it was all hand optimized and changed. The only thing preventing me from open sourcing everything is the possibility of that manufacturer coming after me for violating the original license of their toolchain. Basically if a lawyer can tell me that I can legally relicense everything GPL without risk, then I will. I suspect that this is the case but I'm taking the paranoid approach for the time being. The firmware is really the most valuable and original part of the project, what ties the entire thing together.
The idea that someone would be somehow be "infected" by just using the device in its current state doesn't make sense to me. The hardware and really any hardware is not explicitly licensed. You can always reverse engineer something from the available information. The firmware is currently just a binary blob with no attached license. So again it could just be taken and used wherever. The rest of the software is all Apache licensed which is more permissive than GPL.
EDIT: reading this again I think that you're confusing the hardware and software licensing. There's also some subtlety with different open source licenses. The GPL is the one that may cause you to have to release your code derived from it. Other open source licenses like MIT and Apache allow code to be used in proprietary products. None of the hardware is actually licensed under anything. You're free to do whatever you want with the information about it that is available, including whatever information you derive from studying the hardware itself.
the end user is using part-proprietory stuff
This isn't clearly a problem unless you specify more information about what licenses are in use. You could argue that both Raspberry Pi and Arduino result in the user using "part-proprietory stuff." The Pi has some binary blob aspects of the firmware that are not available in source code form. Neither device has complete layout assets available officially. Some of the schematics are not actually complete as well. None of this prevents people from building commercial products around the devices and also cloning them as long as they respect the software licenses of the software that is available in source code form.
Another way to think about this: you could buy an Axoloti Core but load entirely different firmware on it. In that case you wouldn't be affected by the GPL at all. It's like buying a PC that comes with Windows but then loading a differently licensed OS on it instead.