I think I've figured out WHY I'm shipping this so hard.
The Marten/Claire dynamic has become a healthy version of the Marten/Faye dynamic. The snark is there for sure (the "nice one, Cicero" quote shows that), but without the violence or the sexual tension being used against Marten (and I know, Faye wouldn't have done that to Marten if she didn't have crippling anxieties, which she's now working through, but the fact is, the dynamic wasn't healthy at the time, because of that). Oh, and Claire actually knows when to turn the snark off, and be nice to Marten without a side of snark, unlike Faye at times (like this strip - Faye pre-500 would've given a backhanded insult instead, or maybe even a backhanded compliment). And, unlike Faye pre-500, Claire seems to actually be reasonably mentally healthy, and happy with the direction of her life - and, unlike Faye, extremely motivated to pursue her dream career, whereas Faye is the "underachieving peon" in the service industry, who needs significant help from Dora to even think about pursuing her dream. Claire's motivation could easily rub off on Marten, and make him less of a slacker (although that could work on a friendship level, it certainly doesn't need the ship to sail to do that). (The question is, does Marten have something equivalent to bring to the table? Else, it becomes rather one-sided, like Penelope and Wil's relationship began as.)
Mind you, there's the issue that it's unethical for Marten to date an intern that he's supervising, but Claire has clearly become a member of the main cast, and will probably stick around even after the current interns are no longer at Smif. (How long are they there, anyway? A quarter? Semester? Longer?) Speaking of which, I suspect Gabby won't stick around with the main cast - she's not really been developed at all, and Emily... Emily will probably be brought out for gag strips, just like the robots.
And, yes, there is the potential issue of sexual compatibility, regardless of what genitalia Claire has - Marten did express that his mind would be shattered if he found out that a partner was a trans woman after having sex with her (in the context of Dora), and that case would even be after having genital reassignment. As other posters have mentioned, it's not tactful to phrase that issue as, "she has a penis", though, ever - or to speculate on what genitalia she does have. If that issue ever needs to be resolved, I suspect Jeph will have Claire mention it, using far less crude terminology, in-comic (had to reword that sentence to get rid of a couple awful, and unintentional puns that would have been completely tactless). And, I don't think Jeph will even go there unless it's needed to develop the character of a potential romantic partner of Claire's, as being very accepting (partially because, he's implied that he's not going to write any events that are negative towards Claire being trans) - if the partner doesn't need that development or if she has had genital reassignment, then it'll most likely be left unsaid, and if the partner wouldn't be that accepting, Jeph wouldn't even bring the ship to a point where it matters. But unless that happens, as far as we're concerned, what's down there is none of our business.
Oh, and Jeph did do the "one person wakes up in bed and it looks like sexy things happened but she doesn't remember" gag, which nearly resulted in Marten's death. It was the resolution of the Faye puking in Marten's lap arc.