I think it's a bit iffy to argue that the bootloader code is covered by the GPLv3. In programs for standard computers running a big OS, the distinction lies in whether you are linking a library into your program. If the GPL code isn't a library but an external program, it isn't linking, and OK by the GPL. Now on to the bootloader code: in order to flash your device you have to put everything into a single image file. I guess the claim is that this process constitutes linking. But I don't think that is how most people think. Some possible arguments:

When linking, symbols pointing to addresses are involved. The main program calls functions in the library, and you end up with a whole program. On the other hand, a bootloader just does its thing and then jumps to a fixed address in the main program. The main program doesn't call anything in the bootloader. (Note, the Linux kernel has a special clause that explicitly allows the userland to programmatically interface with the kernel.)

I realize this sort of depends on the microcontroller toolchain. I'm familiar with a few, but not much with STM32 stuff. If the toolchain is dumb and implements the bootloader in a way that resembles linking, i.e. making it possible to resolve all the symbols in the bootloader from the main program then it could very well make the bootloader subject to the GPL.

> This allegedly violates the GPLv3 clause that requires the release of the source code for the entire work if they are combined to form a larger program in or on a storage or distribution medium, such as the flash memory of the STM32F407 micro-controller on the board, and more recently in the update images Prusa supplies

This makes 0 sense as presented here. The GPL explicitly distinguishes mere aggregation from combining in a way that makes it a larger program. Putting both the proprietary bootloader and the GPL OS on the same disk / in the same system makes 0 difference to whether the bootloader is covered by the GPL or not.

If this were true, then any phone, any PS5, any Linux laptop, and almost all consumer hardware would be in violation of the GPL (note that the wording quoted there is also part of the GPLv2, it's not GPLv3 specific).