The only problem with this is that the “theme” is actually hardcoded into the template. Really. Go ahead and remove the theme from the system (completely, remove the theme directory and the entry in webthemes.xml). Do an IISRESET to flush the cache. Create a new site using the template. Bingo. It uses the “theme” so if you ever updated that theme, those sites wouldn’t get the new theme applied.
Although, I do agree that saving a site as a template will do this for you, it also means all sites are running from the database and not the file system which can become a performance hog if left unchecked. 10,000 sites running from a .stp file is sure to be a bigger burden to your system then 10,000 sites running from the file system.