Indeed, the issue is that /etc/thunderbird/pref/thunderbird.js is not
being read. This can be easily confirmed with strace.
Adding pref("intl.locale.requested", ""); into
/usr/lib/thunderbird/defaults/pref/vendor.js makes language
autodetection work again.
As well as adding that preference on a new file in that folder.
Thus, my workaround for the meantime has been to do
ln -s /etc/thunderbird/pref/thunderbird.js
/usr/lib/thunderbird/defaults/pref/etc-pref.js
So that it loads the only preference file I have on /etc/thunderbird
