Some answers about moz.configure

[jfx2006]

Default Browser Agent

Yes, it's a background task thing on Windows that checks to see if Firefox is still the default browser. Possibly other things now. Thunderbird doesn't have such a thing yet.

Bundled Fonts

For Firefox/Thunderbird this controls whether or not TwemojiMozilla.ttf gets packaged or not. That's done in installer/package-manifest.in (and corresponding lines in installer/Makefile.in) -- Incidentally, this is quite likely one piece of your mach package failing on macOS.

comm_paths

I hate these commtopsrcdir, moztopsrcdir, etc things. I added them as one of the first bugs I fixed after joining the Thunderbird team. They're really unnecessary and i plan on ripping them out at some point. They're used by various Makefiles to locate the mozilla source dir (also known as topsrcdir) and the Thunderbird source in comm/. The intent was for those locations to be semi-flexible, but things have evolved and they really are not. So "comm" is literally the comm/ sub directory for the Thunderbird source code. Nothing "common" about it.

newapp_version/thunderbird_version

The only place where CONFIG["THUNDERBIRD_VERSION_DISPLAY"] is used is in about:buildconfig. Elsewhere it's usually CONFIG["MOZ_APP_VERSION"]. This is probably another thing that could be removed from Thunderbird honestly.

Theme Manifest Overrides

Yes, this can be removed. Bug 1372694 removed "heavy-weight" theme support and this is obsolete.