Your post contains a lot of questions and I’m not understand most of them but I’ll try to give you a hint…
I think you know that you can already add what you want in the /etc/skel directory of the template, in order to configure the home directory of user in newly created qubes. Depending on how the application works, it could be sufficient.
You can also use salt to automate the process, run scripts and make sure everything stays in place after the creation process. There is a good community guide on this topic: