Yes, it will be handled using same system.
The design with be that the editor is rich text, but when you save the file it will be saved as plain text. The rich text spans will be saved using Markdown formatting.
I’m pretty sure this will happen in TaskPaper 4. But I’m pretty sure that’s still a long way off. In the meantime I’m working to make the same system work for WriteRoom 4 which I’m working on now. In the meantime you could use Markdown formatting in your Taskpaper document to (for example) bold text. Then later whenever TaskPaper 4 comes around that formatting will appear as bold text. Instead of just plain text sourounded by **'s.