You are playing your normal game of semantics. To me it is pretty simple. You found the joke to be objectively transphobic, I did not. Subjectively perhaps, based, as you said, on preconceived notions, but not objectively so. I did not find the penis to be the punchline, you did. That is your perception, and that is my perception in a nutshell. We can agree to disagree.
We can also agree to disagree about comedy and offensiveness. My wife found a group of people on facebook (sorry, on "Meta") complaining about Jim Gaffigan of all people. Blew us away. Found much of what he did to be body- and fat-shaming, and such. Just because you find something inoffensive does not mean that no one else does. You grossly underestimate the human animal's ability to find offense, and overestimate your own ability to judge offensiveness for others.
Here is an interesting question: as long as even one person can be offended by something, should it be eradicated, and everyone who is not offended villified?