I've always thought that just like you need an Extended License if you want to use a WordPress plugin on a WP Multisite the same would go for a WordPress Theme - you will need to get an Extended License. However if you look at the Extended License for a theme and a plugin you can't really compare!
The problem is that if we create a WordPress plugin specially for WP Multisite we can't just sell it under the Extended License - so some people just buy a Regular License and then use it on their WP MS.
I guess you are in exactly the same situation with themes, but could you do themes for the different versions? (WP single site and WP MS?)
We have many of people contacting us about developer licenses for plugins, which is not available. I presume you Theme authors are in the same situation.