I think we are miscommunericating

Obviously this plugin is most likely to be used by superadmins in multisite, why else would it exist?
I am developing a range of templates for standardised content across multiple themes.
I created a dummy blog and set this up. Created a template from that. Changed all the theme settings and made another template for another theme and so on. This was a very silly way to spend a weekend!
Of course it mashed up every change and turned the new templates into a conflicting mess of settings.

The warning on the plugin says "Please note that this will turn the blog you are currently logged in to - http://artsnet.co - into a template blog. Any changes you make to this blog will change the template, as well! We recommend creating specific "Template Blogs" for this purpose, so you don't accidentally add new settings, content, or users that you don't want in your template."

But that is false. As superadmin I had the dummy blog admin open but it is implying that I am logged in to the main site.

If I am understanding the remedy for what I did wrong... I should be creating a new blog based on the template made from the dummy site, then change that blog and make another template from that. Repeat and rinse.

The implication of that warning is by doing this I am changing not only the 'Son of Dummy' blog but the Dummy template as well. Which would suggest that the only clean approach is to start almost from scratch each time, which would make the plugin pretty much redundant.

Hoping I have not confused you as much as I have me.