So I played 0.3.3 and got my ending. For the sake of understanding: Can you plug in an ending in CS2, finish it, then go back to 0.3.3, get a new ending and plug it into CS2 all the same?
Yes. Whatever's in DataCrystal.js gets read into 2 fairly early on (though not immediately) in a given game, and after that it's locked in on that save file. But if you start a new game, with a new DataCrystal file in place, it will go off that DC file instead.