Okay, I see what you're getting at, LivingInGrey, but I don't think it's nearly as much of a problem as the gender marker. You basically can't change the gender marker with the SSA unless you've had genital surgery (or for the guys, top surgery), but a name change is a piece of cake compared to that, even for low-income folks. And you can change your name at any time during transition or even before you start transition; I know countless people who changed their names well before they were "passing," and that includes me. Some of them are women, so I'm not just speaking for the guys. Seems to me that if you're already living full time as a woman and are going on job interviews while presenting as female, maybe you should have legally switched to your chosen name by that point.
I just don't think it needs to be an issue for the vast majority of us. I suppose it would be nice if you could register an alias with the SSA and not have it come up as a mismatch...was that what you were thinking? I expect that such a scheme would make identity theft that much easier and cause a lot of grief for both the SSA and individual citizens. The easy solution? Change your name when you start going full time--or even before--and just use your old name informally for as long as you need to.