Sure, Qubes strongly discourages running software in the distro templates (eg, debian-11, fedora-34), so there will be nowhere to put the user.js file since one needs to run firefox to build the /home/user/.mozilla directory. The Qubes templates doc even mention firefox in particular:
A template should be used only for installation of packages, and nothing more, so it should never get a chance to actually run
/usr/bin/firefox and get infected from it, in case it was compromised.
As I understand your post, you’re creating an appVM and using it as a disposable template, by, for example, checking the “Disposable VM Template” box in the qubes settings of the appVM. This method is what I was also recommending, but each dispVM will reuse the same firefox profile created in this appVM. I’m curious to learn if firefox policies allow for a way around this weakness, sounds interesting…