The fact that subcultures can be voluntary, whimsical, or ephemeral doesn't mean they have to be, and I certainly don't assume any lack of seriousness or significance to the notion that someone is a member of this or that subculture.
That is not at all what 'radical' means in the context of 'radical sub-culture'. The definition you're looking for is one of:
2. thoroughgoing or extreme, especially as regards change from accepted or traditional forms: a radical change in the policy of a company.
3. favoring drastic political, economic, or social reforms: radical ideas; radical and anarchistic ideologues.
I guess you could argue that trans people fall under definition # 2 from the perspective of many (most?) people, but i also think that 'radical sub-culture' generally implies some kind of conscious action — i don't think that simply existing as a member of a minority makes you inherently 'radical'.
If you're not sure what someone means, consider asking them rather than complaining about it. Transitioning to a different gender from one's birth default is (for the time being) a radical change involving extensive medical evaluation, a lifetime drug regimen and ultimately major surgery, to say nothing of the social difficulties.
Neither have positive connotations, but "fundamentalist" is worse. Fundamentalism specifically invokes ideas of religious fundamentalism, particularly "religious right" style protestant beliefs.
"Radical" on the other hand is used in a more diverse set of cases. It invokes thoughts of any number of political or religious beliefs that are either outside the mainstream or do not conform with progressive western values as they are traditionally stated.
I don't think either is dismissive. Descriptive, with negative connotations, but being critical is not the same as being dismissive.