Did you forget Multisite support...again?
The Warp framework finally got around to supporting multiple styles which solved this issue... However now with Yootheme Pro, you're reverting back to having the theme writing all it's style to a single file. This makes Yootheme Pro useless in a WordPress multisite environment.
I was hoping the new feature "style library" would solve this. But it did not unfortunately...
Yootheme pro supports custom less..why not write the output into i.e a file for the profile instead of a shared theme.css file? I.e. we create /less/myprofile.less, then the output would be saved as theme.myprofile.css. There are numerous ways to solve this and support a multisite installation. Please don't just ask me to add it to the feature request thread..this is something you should've implemented when launching Yoothem Pro.