Time Out Chicago has a great Q and A session with Jane Lynch in which Glee is used as a starting point to talk briefly about being a tomboy, being more femmey, and her lesbianism in general.  On being asked whether she ever identified as trans:

No, because I was too young for it to become that big of an issue. I know some people feel like they’re in the wrong body. I completely understand that, but I started to accept my feminine nature more as I got older—and love it, too. In A Mighty Wind, I played this very sexy come-hither woman, and it really released me and got me in touch with my own feminine wiles. And it’s been lovely ever since.