When you create an AppVM it can inherit from its template. This won’t keep your dotfiles synchronized after AppVM creation but it does provide a starting point.
Beyond that, for networked VMs, you could sync your dotfiles from a version control system (you should be able to find some examples online of how others have achieved this) or from some other remote source.
For network-isolated VMs, I’d probably handle those on a case-by-case basis. For example, I really only open my vault app in Vault so I probably wouldn’t need to worry about dotfiles. In a less sensitive, yet isolated app, I might just do the occasional copy between VMs.
Others have configured things such as Firefox profiles and configurations from a template, too, in case that gives you additional ideas.