You don’t have to use the wizard for templates that have a specific folder structure. The system for searching and replacing is role-agnostic. Which is a fancy way of saying you can do pretty much whatever with it.
You can use it for settings files, project READMEs or other files (and folders) that expect some form of information that is always the same, like for example the author name and the name of your organization.
You could even write a snippet of code in your rules file that gets the names of all QuickTime .mov textures in some project’s tex folder and use a line seperated listing of those names as a value in the RULES dictionary that will be read from the rules.py file.