That suggestion makes sense, but I'd be sorry to see the UI get more complex. I suppose a "mode" might sufficiently encapsulate SmartEdit, but it could get confusing. That said, I've always wished I didn't have to export to SmartEdit and then import back into the editor I'm using, so the idea certainly has merit!
For the record, all my text ends up in InDesign, and going back and forth from InDesign is not a simple thing -- nor would I want to do it at all, if it could be avoided. So having all or most of SmartEdit inside Atomic would at least eliminate one whole category of round-tripping.