I know I'm not the center of the world and I usually try to see the good side of things that are not my cup of tea, but I'm really having a hard time here.
How can not mainlining the sources be a good thing?

I'm sure if they just dumped the code somewhere under a Free license as it is someone would pick it up and mainline it.
It's so easy that not doing it can't even be attributed to lazyness.

I can't judge System76, but I'm not all that impressed by Purism in terms of philosophy.
Sure, they occasionally release a nice piece of HW, but I think they are making way too much fuss around it compared to what they actually deliver. In my eyes it's far beyond "good marketing".

The same thing could be said about the N900 8 years ago, and look what we have now:
A device running hopelessly outdated software (in terms of security, not end-user features) that was basically broken right from the start (Maemo is, and has always been, dependency hell at its worst).
No other ~10 years old system I still run (and I run some) is in such a bad shape software-wise.
The only redeeming qualities that still make me use the N900 are 1. that it happens to be able to make phone calls, 2. that it fits into my pocket and 3. that there are no other devices fulfilling 1 and 2 while still giving me a GNU/Linux system of some sort without running an OS underneath it that is known for spying on me.

So no, with respect to the N900 story, a device running Linux on a non-mainlined kernel does not qualify as "running linux very well" in my book.