I finally found it, after looking at literally over a thousand ebooks in my library. My description was close but not exact. The main character (you, being that it's told in the second person) is a passenger on the spacecraft, not crew, and doesn't rent a room.
The story is "Second Person Unmasked" by Janis Ian, first published in the 2003 anthology Stars: Original Stories Based on the Songs of Janis Ian, edited by Janis Ian and Mike Resnick.
Summary from here:
You probably wouldn’t expect it to inspire a story about a planet-hopping sociopath forced to undergo a sex change. But it did: Ian’s “Second Person Unmasked,” which appears in the anthology Stars: Original Stories Based on the Songs of Janis Ian.
The "he" in that story (written, effectively, as “you”) carries a spring-loaded double switchblade, wears a belt with a sharpened buckle and has a high forehead, which in Ian's words has “don’t-fuck-with-me written across it in lines that took decades to accumulate.” He’s an obvious predator -- a literal lady killer -- and from his homophobia to his conquistador walk, he’s easy to hate.
But then, when two blonde girls with silver necklaces seduce him, trap him, and ship him off in a cargo freighter; when he’s sold into slavery, re-educated, starved and then changed into a sociopath-trapping girl himself, you start to pity him. Not really — "he" was terrible, even if "she" isn't — but the story plays with your initial repulsion. Like the song, it takes a hard look at both the cyclical nature of abuse and the structural links between gender hierarchy and violence.