I think it's an interesting dichotomy. As so many others who probably AREN'T regulars on this thread have said, "You know, if Jack got rid of those tattoos, grew some hair, and wore something a little more normal, she'd be pretty hot." I think a lot of how Jack chooses to look is an attempt to completely sublimate her femininity, which she sees as a sign of her being "weak."
She's reached this point where, deep down, she blames herself for everything that has happened to her in the past, because she wasn't strong enough. So any sign that she's "girly" or something like that gets suppressed. Hell, even her name is a guy's name. Yeah, she had it back in the facility, but it would have been easy enough to pick a new name once she had escaped. The fact that she still goes by Jack is both an indicator that she wants to be "masculine" and, in her view, "strong," and also that she hasn't left the facility behind her, and that no matter how far she runs from it, it's still a part of her.
Or, as they might say in the Tali thread, "Yeah, Jack's awesome!"