VR configurations are saved. All configurations are, but VR is separate.
We, deliberately, allow users to make the choices for their configuration. We support so many different controllers it is impossible to know what the user wants as defaults.
We do make it easy for users though. In Options->Controls->Map Controllers, have you tried selecting the Touch controllers from the drop down list, then press the "Default Map" button?
It may not work, as all VR controllers are handled specifically, unlike regular input devices. I really do not know of anyone using the Touch controllers as their primary devices for flying in Aces High. Would like some feedback, if you chose to do it.