So, I'm a bit confused as to what would actually be okay and what isn't here.
For example, there are numerous stand up shows or comedic acts that take the piss out of different races. Being Indian, I know Russell Peters is probably a good example of it. He makes jokes about every race, but I'll focus on the ones about indian people for simplicity sake.
The jokes, whether you find them funny or not, usually attempt to cement some stereotype or create new ones.
I love Russell Peters, but I think that last sentence is where you might be off. The heart of Russell Peters' act is discussing and laughing about stereotypes. He does not attempt to cement stereotypes or create new ones in earnest. Peters makes jokes about or involving stereotypes (which are often somewhat offensive in of themselves), partially to make fun of that stereotype, and partially to uncover where the truth lies in that stereotype. He's a great act because you're going in knowing, "Okay he's probably going to make jokes about my ethnicity and the stereotypes about it, but I know that going in, and he's going to be making jokes about almost every ethnicity and their stereotypes too."
It's about context and purpose of delivery. When you watch Russell Peters, do you get the impression that he doesn't like Chinese people? That he thinks black people are beneath him? Of course not. Now, when you watch that Chappelle clip, do you get the impression that he feels transgendered people and their cause is fully legitimate?
And to be honest, I don't know what the correct term would be. If I wasn't able to tell what orientation a person was, is it so wrong to just take an innocent guess based on characteristics that you have [for the majority of your life and possibly applicable to the majority of people in your life] associated with a type of person? Wouldn't the next logical step for an observer to then correct them, and if they don't get it, explain why that's wrong or offensive?
It's totally fine if you don't know the correct way to address a trans-gendered person (hell, I don't know half the time either). And if you do get it wrong, and they get mad, I think it's okay to get a little upset if you were apologetic and were trying to accommodate their identity in earnest.
None of that is the problem with Chappelle here. The problem is when he starts off the joke joking about calling them trannies, then finishes off his anecdote that he believes trans-gendered people are living in a fantasy world, and being trans-gendered is the same as a black person pretending to be white. THAT is the issue here.
All of that stuff about Dave feeling upset that he got accosted for messing up his pronouns is fine, even somewhat funny. The problem is - at least via his delivery of the joke/anecdote - that he was upset not just because of the overly-political correctness of our current society, but because how dare this tranny get upset with me when I'm the one who has to indulge in their fantasy about their identity, which isn't real.
THAT is the issue with the "joke".