Yes, anything in /etc/pulseway will not persist after a reboot, so you should always edit the one in /boot/pulseway. That said, if you just want to test that your config.xml changes work, you could edit the /etc/pulseway file so you don't have to reboot after ever change
Correct, just place the new version in that directory and it will be installed on the next boot
See #1
I've seen this warning as well but as you mentioned Pulseway is not available via NerdPack. I believe putting the package in /boot/extra is still the recommended way to install packages at boot, so you should be able to ignore this particular warning
Hope that helps!