I think this is a "What if" scenario with the characters from the author other manga Genshiken and Genshiken Nidaime, both focus on this university club/circle of otakus with the same name, Genshiken, the manga keeps goings as people leave and enter the club as their years of Uni happens.
There is a character, Madarame, who develops a crush on the Girlfriend of his Friends, Kasukabe and Kousaka, at some point he is honest with his feeling, knowing fully well she is going to turn him down, and its more about going forward after the rejection.
Later down the line, a Crossdresser, Hato, joins the genshiken, and while he thinks or says he is straight nor is trans and just crossdress, hato ends up falling in love with Madarame,
To my understanding Spotted Flower is a what if scenario if later, down the line, Madarame and Kasukabe did end up together. While never actually stating they are the same characters