Disney has not made any announcements but this is my guess as to how it will work.
Transportation will still be free with your resort stay. So instead of taking a bus you will take the train. Your baggage will still be checked through to your room.
You will then catch a bus at the station on Disney property but the difference is you will have the option of going directly to any resort (dinner reservations etc) or theme park (you would already have your length of stay passes or they could be picked up at any 'guest services' with proper ID) or you could be taken directly to your home resort (Magical Express does not offer this service) or you may be going directly to DTD.
Since Disney will know exactly when each train is arriving, they will be able to have transportation waiting at the station. They will also know the numbers of guests arriving with reasonable accuracy so a seat will be assured.
Finally, the trains will be reliable and punctual. ME can't make that promise as it depends on I-4 traffic conditions.
The benefit is that this will relieve traffic on I-4 and reduce wear and tear and possibly eliminate the need for further widenings after those already scheduled. I just read it will cost 3 BILLION DOLLARS
to widen I-4 from Tampa to
just Lakeland if it becomes necessary again. That is more than the cost of HSR from Tampa all the way to Orlando! HSR is a no brainer, at least in this instance.