I feel like you missed the whole point about Natsumin. She really was never a background character. Even when she didn’t appear directly, Sunao or Lemon were always talking about her. She was always the center of everything for Sunao.
She's not just nice, she's also cute, understanding and genuine. Lemon felt lacking and couldn’t truly connect with others outside of Sunao. Natsumin is the person who healed her wounds, made her want to change and also a precious friend. She mentioned several times how she was envious of her and how she admired her.
For Sunao, who promised to never love again, Natsumin was someone so genuinely kind that he fell in love again. She was someone that he couldn’t ignore.
You say she's not special, but she truly is. More so than Lemon if anything. Lemon is your "typical" beautiful, smart and nice protagonist. She has nothing more than Natsumin. You say Natsumin is "just" nice but what about Lemon? Isn’t she "just" the same by that logic?
Same goes for Sunao too. He's not striking or the smartest but he's kind. They're all just cinnamon rolls.
I think you're just too focused on "but Lemon and Sunao are the main characters, they *have* to be shipped together. Main characters go with main characters". You fail to see that Natsumin is a core character with lots of redeeming qualities that both main characters deeply love.

OK sorry but this was an awful ending, 80 or 90% of the story was about Lemon and Sunao, Kagohara was pushed back constantly, she was just there, her chemistry with Sunao was basically non existent, and she wasn't developed at all, and the ending itself...
We got 100+ chapters with a body swapping, and it was fixed in last 2 or 3? Come on?!
Tbh I want my time back! Yes I liked Lemon as a heroine more, but I believe most of the ppl though the same, since she was front and center for the most of the story, while Kagohara was just a nice girl, nothing special there, she is pretty and nice, that's it.
Still I was sure that Kagohara will end up with Sunao, but I was hoping that at least author will do something with her before the Manga ends, but nope, she is so damn vanilla that it's insane till the end, so sorry but with this ending I would prefere to see Sunao x Lemon end, because what we got was a complete joke.
Even in last chapter Sunao tells Lemon that he started to like Kagohara because she is nice, no wonder, because you can't think of anything more that that, if we could get idk like 5 or 10 more chapters focusing solely on Sunao and Kagohara and their couple dynamics I would be more than OK with ending but the chemistry is just not there.
Sorry for a rant but damn I was expecting way more from the ending.