If you don’t mind, I recommend commenting out the defer_parsing_of_js filter while you work in Microthemer. I would need to do some serious testing and debugging to make sure that there are no unwanted consequences, aside from the ones you noticed immediately. This would slow down some priority tasks we’re trying to get finished right now.
But when we start work on the speed optimisations and general reorganisation of the code base, which will entail a deep test of all functionality, I’d be happy to see if MT can work with deferred scripts too.