@amoroso 'DBusActivatable' means gnome will try to run it via dbus-daemon (the user-level one, not the system-wide one) and not directly, i.e. it's actually closer to one of the following:
1) gapplication launch net.trowell.typesetter
2) gdbus call -e -d net.trowell.typesetter -o /net/trowell/typesetter -m org.freedesktop.Application.Activate {}
which will cause dbus-daemon to run the process as configured in /var/lib/flatpak/exports/share/dbus-1/services/net.trowell.typesetter.service (if it's not yet running), and then deliver it a D-Bus message saying "open a new window".
since it's really started as a child of dbus-daemon (or a child of systemd --user, depending on distribution) it will inherit different environment, which might have stale envvars from the previous session (though the new session ought to have overridden them...), so compare the "first" and "second" session environment from:
systemctl --user show-environment | sort
and also try to run the 'flatpak run' command as a child of systemd, i.e. first do:
systemd-run --user --shell
...and then the whole 'flatpak run net.trowell.typesetter' within that nested shell.