When you create a VM based on a TemplateVM, the gnome-terminal settings (font, color) are not inherited by default. This document describes how to set terminal defaults for all VMs subsequently created off a TemplateVM.
(Previously-created VMs are unaffected.)
This document only applies to gnome-terminal (the standard terminal) and not XTerm, etc.
Thanks to unman on qubes-users for explaining how to do this.
In dom0: qvm-run MYTEMPLATE gnome-terminal
In the terminal that pops up, adjust settings to your liking.
In the templateVM's terminal:
sudo mkdir -p /etc/skel/.config/dconf
sudo cp ~/.config/dconf/user /etc/skel/.config/dconf/
sudo reboot
Subsequently-created VMs should now use the chosen settings by default.