I don't think anyone knows outside of those working on the project.
But ever since I heard that they were adding a ceiling to the SM boarding area, I did my own "armchair Imagineering" and made a few guesses on how *I* would do it...
I picture a high ceiling over the boarding area. There's no ride track above that, so they have all the room up to the dome ceiling if they wanted to. Perhaps it would start low just above the ride track, and then angle upward to meet the dome above the TTA track. The TTA would ride through this boarding area that's themed to the inside of a space station. Perhaps there would be more lighting up above so that the people waiting in the queue could actually see the TTA cars more easily, rather than just something moving through the darkness as it is now. Kinda like how you could see the PeopleMover trains going past the Star Speeder in the first room of Star Tours' queue at Disneyland.
Then, the TTA trains would pass out through an opening, out of the space station and into "space" where they would see the glow-in-the-dark trains zooming around the track like they always have.
The TTA has a pretty long stretch of track after the boarding platform. So even if they incorporated the TTA track in the newly-roofed-over SM boarding platform, there's still plenty of time to look into the ride area itself afterward.
-Rob