I see a few people saying that the original limerick had nothing to do with transgender people. Just thought I'd throw in my two cents to try and explain how the other camp sees it.
For male-to-female transgender people in particular, being "found out" can have really dangerous consequences, and many, many of them have been killed because men find out they're transgender and fly off the handle. Not because the women led them on or "tricked" them, just because the men felt insecure or embarrassed about having displayed interest toward or had sex with someone they now perceive as male. Google Gwen Araujo, Nireah Johnson, Angie Zapata, Dee Dee Pierson... it's a legit concern in many transgender women's day-to-day lives and something they have to think about whenever a man shows sexual or romantic interest in them.
Jokes like "a man found out the woman he slept with was actually male and freaked out, har har" perpetuate the idea that it's reasonable to freak out after mistaking a man for a woman, or a transgender woman for a "biological" woman.
I agree that the limerick could refer to something else in the game world -- hell, maybe a man just put on a magical Girdle of Femininity or something, no transgender people need to be involved for it to make sense -- but to the people who were offended, the limerick perpetuates the idea that "gay panic" or "trans panic" is something funny/acceptable, and I think that's what many were objecting to.
As a transgender man, the limerick made me roll my eyes, because it's the kind of stupid **** I had to hear over and over again when I was younger. I wouldn't write to the devs about it, but I can see how others would be disappointed to see it, and I'm impressed both by the devs for taking action and by the backer who wrote the limericks for reacting with humor to the situation.