Basically I want to set up a template where I have the option to enable or disable a plugin on the window where we select a template. Is that a possibility?
Coming back to answer this for whoever does stumble across this same problem, it is possible.
All you need to do to is add a
HiddenSettings=(Setting Name)
to hide it. ALternatively, you can unhide it by removing it from the TemplateDefs file.
Hope this helps whoever is new to setting up templates.