Now that I think about it a bit more and honestly hope I'm wrong I think this is Tsubame-senpia's answer to Ishigami's confession. The answer is no but Ishigami will once again have a proper chance at love.
My idea is that Tsubame knows that once she graduates after she turns him down is that he'll be sad no doubt and knowing that people won't even give him a proper look in his grade will severely hurt his chances of any girl giving him an honest look without any prejudice. She herself was warned somewhere if I remember right.
But with this Tsubame will unlock the potential for Ishigami to find love somewhere else without any prejudice. Sincerely hope I'm wrong because this feels like there's something else mixed in here like when Tsubame just tossed herself to Ishigami to be nice, can't remember the exact reason, and it feels like a roundabout way of rejecting him.
God I hope I'm wrong.