It's presented that way because Setsuna is the secondary protagonist of this game. Not just the main female heroine but we literally view the first half of the story from her perspective. There is all this great extra stuff too but the main point of the game was to give Setsuna her own route since she didn't have one in he original School Days. So if you get any other girl's ending it means Setsuna loses after all that early game buildup which is always cannon so there's that bittersweet vibe to it.
There are technically some more Kokoro endings but the one you got was the most legit one where they might become a normal couple. That scene with Kotonoha makes me think there was suppose to be some choice with an ending split there but they must have cut it out so you only get the one ending. I'd definitely like to see that ending expanded so we get to know whether Kotonoha eventually gives up or if Makoto just ends up dating both sisters. Also a more standard Kokoto route where they properly date would be amazing too.
Not that I'm expecting them to actually make anything more for this series unfortunately. What we do have is still pretty great though. A whole game made for a side heroine like Setsuna is basically a miracle.
