My template is debian based so /etc/skel should be fine. My understanding is that qubes makes a private volume that it mounts into /home and some other dirs but thats the only non volatile part. When u create a new app vm from the template vm the private volume of the template is thrown away and a new one created this should create a new user that should be templates from /etc/skel but thats not happening idk why
You're looking for something hyper specific. I'd say check in the forums like the other comments said. Else actually debug and check that the file you mean to exist actually exists on VM boot. You have a chicken and egg scenario, and the first step is logs.