Didn't think about that. They are basically different versions of the same game. You will get all the Trinity goodies in Rebellion, just a different way to go about it. But if someone buys Rebellion, will you be able to play Trinity without the Rebellion extra stuff?
When Diplomacy came out, you could still play a Entrenchment game from within Diplomacy.
Apparently, from what I have heard, the testers they brought in before the beta were confused by this, so now you have to declare your allegiance before a match. I don't have a problem with being able declare your allegiance before a match, but if that is the only way to play I am going to be very disappointed.
It doesn't seem very complicated to me, they could make it like Command & Conquer: Generals: Zero Hour, where all factions could be selected, including the original ones, and they could even reuse the selection screens they have now as the in-game facilitator for declaring allegiance, but then what do I know.