As I've mentioned before (in fact, I created this account to post about it a few weeks ago), I'm MtF transgender, and it's been my observation and the observation of the trans communities I participate in that a disproportionately high percentage of MtF trans people work in the tech industry and/or are tech hobbyists. The "MtF computer geek" is in fact one of the most prevalent -- and in my experience, one of the most true -- stereotypes of trans people I've seen.
I'm reminded of the old Russian meme, where one person wanders into an anime IRC channel and asks "Hello, is this an anime channel?", followed by "How do I patch KDE2 under FreeBSD?". It became a popular meme because it's true: anime fans tend to be computer geeks. I've also seen this same exact joke posted in trans communities, by the way...
(Oh, and lest I forget, a huge chunk of the trans community is into anime, too.)
There is something about certain characteristics that heavily draws people to the tech industry.
If you're trans? If you like anime? If you play sports like Ultimate and rock climbing? You're probably a techie.
Honestly, I've noticed that for many of these (e.g. anime, Ultimate), the inverse is true as well, and if being trans wasn't hard-wired and such a tiny, tiny minority of the population (most estimates I've heard are around 0.3%), I'd bet a huge amount of techies would be trans.
I think of all the theories OP proposed, the most likely one is that "programmer culture" is a distinct subculture much like e.g., "academic culture".
Of course, there are a few reasons for that. If you look at ESR's "A Portrait of J. Random Hacker" (http://www.catb.org/jargon/html/appendixb.html), he absolutely nails a personality type that goes into some of this. The section on sports, for example, goes into how hackers are drawn to sports that focus on self-discipline and technical ability.
Another is that tech stuff is looked down upon by society. Mainstream society sees us as weirdos to be shunned. You know who else societies see that way? Anime fans. Trans people. By and large, all three communities are very accepting of cultural differences. For example, techies will happily accept trans people into their communities because they know what it's like to be marginalized. And I think LGBT people are more likely to hang out with communities focused on marginalized hobbies than other minorities, because of how we're perceived. Racial and ethnic minorities are set apart because of how they look and sound. LGBT people, on the other hand, are set apart because of what we do, and "set apart for what we do" is also a good description of how techies and anime fans are separated from mainstream culture.