I suspect that it is part of the joke - for someone so obsessed with genderroles and the true way, she clearly isn't in a happy relationship.
Maybe he left her for another man.
According to That Other Wiki, that's pretty much the case. He ran off to San Fransisco.
Megan was supposed to always have been gay, but the reasons she was sent to True Directions seemed like a weird way to get her there. Eating tofu and not wanting to kiss a boy who is a disgusting kisser in the first place... can you really identify her as gay just by that? Maybe that was the point, but she really is gay, so... did Dumbass Homophobes Have a Point, or are we not getting something here?
I think those "symptoms" were just a coincidence. She could have been eating vegetarian to try and keep her weight down for cheerleading. Her boyfriend being a bad kisser might have been exaggerated though; the movie is from a lesbian's point of view, after all.
Her boyfriend being such an awful kisser is probably mostly her opinion because she's completely disinterested. With the power of omniscient camera, we know she was always thinking about girls anyway. It's possible her friends and close family saw more signs of this other than just the locker pictures, but going into those would have slowed the scene down and made it less funny.
I thought they were a parody of whatever random attributes people tend to identify as "gay". It's a bit of a Hitler Ate Sugar thing. Some gays eat tofu, therefore all tofu eaters are gay.
Is Jan straight and cis, or an FTM? I always assumed the latter, but apparently not everyone saw this.
I don't see her as a transman. She seems like a boyish girl.
My interpretation was that she wasn't sure either until the outburst scene; that she'd been accused of all kinds of things and was mixed up about her own feelings, especially if people had been telling her that she couldn't be a girl if she behaved like herself. Finally she realises this is nonsense, that she's both straight AND extremely butch. Genderqueer maybe, but not a transman.