If I change a config file in /etc, will the changes survive a reboot?
I didn't completely understand how etc is handled, but it worked fine and kept my configs while merging at the same time the files from the apps i installed
How can I see or decide which parts of the system are immutable and which are not?
I'm note sure it's possible, at least i didn't see the option and i've never tried (i never needed it anyway). /var was mutable, /usr/lib /usr/bin... were not (/usr/local was mutable), and /opt and /home were symlinked to /var/opt and /var/home, so mutable
edit: now i remember there was something about using "overlays" that allowed to modify /usr, i think i only used it once so i don't really remember
Can I install packages that aren’t available as flatpaks, like more obscure stuff or command line tools?
Yes, thanks to rpm-ostree, you can install basically any rpm with it, it's just really slow as each transaction must create a new generation, but it worked fine. Also you are supposed to reboot to make the changes apply, unless you use the --apply-live option (which was described as experimental when i was using it, don't now about now tho)
What about ppd files for printing, firmware, drivers, fonts, icon packs, etc.? Where and how do those get installed?
Same thing, rpm-ostree