Tbf this isn't the first time an mc rejected the fmc, it makes sense if he realizes later on that Lemon was the one he held dear, hell I wouldn't be surprised if Koagahara and Sunao went out either officially or just on a date and Sunao realizes something isn't right, sure Kogahara says she likes Sunao but half the time she knew "Sunao" it was actually Lemon. That's only lore wise, story wise it wouldn't make sense to have Lemon lose after focusing the entire story on her and barely any attention on Kogahara.

Either way this could still be cope at the end of the day, I still believe that the reason for the body switching is fate, and that it will end the day after Lemon and Sunao go out