Microthemer should work fine with Divi, or themes that use shortcodes. Theme shortcodes produce regular HTML output when the page is rendered. Microthemer is able to target any HTML on the page. It makes no assumptions about the kind of HTML a theme will output. It just deals with whatever it finds.
Microthemer’s selector wizard isn’t perfect though. If a particular section of HTML doesn’t have any uniquely identifying classes or ids, it will sometimes be hard to target one element in isolation (as opposed to a set). The next update to the selector wizard aims to improve this by presenting :nth-of-type selectors. Also, if my memory serves me correctly I think the Divi theme allows users to insert their own ids which would make it play well with Microthemer.
I hope that helps. Please let me know if you have any further questions.