At least in its Feb 18 incarnation, /usr/bin/qubes-run-terminal has this order hard-coded (regardless of any environment variables):
- x-terminal-emulator
- ptyxis
- gnome-terminal
- kgx
- then a list of “xfce4-terminal konsole urxvt rxvt termit terminator Eterm aterm roxterm termite lxterminal mate-terminal terminology st xterm”
So… hard-coded.
It is a Bash script, you can read it too. 
Maybe the solution is to change the “alternatives” (in the template) of x-terminal-emulator to point to gnome-terminal?