Yes, Rebellion will have all the features of Trinity by itself. What we don't know is if you'll be able to play trinity by itself if you wanted for say mods and other things.

It might also be possible that a couple changes will be made to Rebellion that won't be ported back to the older versions of the game.  The biggest issue in my mind is whether someone who purchases Rebellion without having owned a previous Sins game would be able to load up Vanilla Sins, Entrenchment, and Diplomacy.