Can't customise before first launch

I'm installing ubuntu server on to a few machines and then running some bootstrap scripts to customise the install, part of which is to add some custom configs to byobu - I want to add some keybindings to .byobu/keybindings/f-keys.tmux and "set -g mouse on" to .byobu/profile.tmux

The bootstrap scripts are run as root on a completely fresh install, so I enable byobu with sudo -u <mydefaultuser> byobu-enable and then cat my configs into the files mentioned above. However this seems to prevent byobu copying in all the other default configs into .byobu, I guess to stop it clobbering an existing config, so is there a way to trigger the creation of the default config files without having to login? Or can these custom keybindings go somewhere else?