X sansmerci
OP, you're letting your perceptions of gender roles bleed into thinking about queer folks.
A woman in a flannel shirt is still a woman, there is nothing in particular about flannel shirts that is for men only, you just associate them with what's acceptable as male presentation. Same with men who have traits that are considered feminine. There's nothing about caring for one's appearance, for example, that's particular to woman-ness; historically (wealthy, privileged) men have had much more freedom to decorate themselves.
Not to mention that, while there is nothing wrong with acting or dressing in a way that doesn't 100% dovetail into gender roles, it's neither exclusive to homosexual folks nor does the varient you're talking about account for the vast majority of the community. You just notice those gay people more because you're already paying attention to how they act/dress. If you see a woman who is dressed androgynously with her boyfriend, you don't make note of it because it doesn't fit, and so your mind stores away the perception that less traditionally feminine presentation is a lesbian thing.
Your comment reminds me of a conversation I had with a friend about how certain style/fashion elements "prove" a person is lesbian.
He told me a lesbian is easily recognizable because she wears flannel. I went to my closet and fished out a white flannel, Victorian styled nightgown smothered in ruffles, lace overlay, and satin ribbons. He quickly clarified, "No that's not what I meant. I mean plaid, workman styled shirts." So I dug a bit further and pulled out two long-sleeved, button down pink and lavender plaid shirts I use as jackets in the cooler months. THEN he said, "No, those are all pink and girly. It's REALLY blah-blah-blah...."
The thing I find harmful about all this "sexuality stereotyping" is that it leads to confusion and misunderstanding. I'd hate to imagine a gentleman I liked giving up on me because something in my appearance or my behavior struck him as "lesbian" according to stereotype.
I wonder if the LGBT community stereotypes straight people. I need to ask some of my LGBT friends about that.