You can’t delete a domain from your quota. The standard license permits installing Microthemer on 3 sites in total, not 3 sites at the same time. So it’s not possible to transfer site licenses. This is because it’s a feature of Microthemer that you can completely uninstall it after making style edits, and still have the changes stick. See MT’s Preferences > Inactive tab for more information on that. As such, there would be little advantage of the developer license if the standard license wasn’t for 3 sites in total.
Once you’ve installed Microthemer on 3 domains, you will need to upgrade to the developer license via your dashboard to install Microthemer on an additional domain. I hope that makes sense, and sounds reasonable.
Please let me know if you have any further questions.