I created a blog template with New Blog Templates. The template had a third party plugin activated with custom settings of that plugin. When I manually created a new site as a free level site(from the network admin dashboard), and chose the template, the plugin and all of its settings transferred how it was supposed to.
I have the premium plugins manager module enabled, and, for this plugin, I give access to the free level and the middle level, with the top level check box unchecked to disallow access to the plugin for the top level.
When I manually changed this site's Pro Status level (from the super admin dashboard) from the free level, to the top tier level, the plugin that I was trying to have deactivated remained activated and all the settings intact, even though I had the box unchecked in the premium plugins manager settings for that level.
Then, while trying to troubleshoot this, I manually removed the pro sites status for this site back down to a free site. At that point, the plugin did deactivate. However, when I tried to manually change the site level again, the plugin wouldn't reactivate on any level.