Perhaps the most obvious answer to this is “Man Enough to Be a Woman” by Jayne (formerly Wayne) County. Probably other songs by her as well.
These are not necessarily positive in their reference but a reference nonetheless
Eazy E - Nobody Move
NOFX - My Vagina
Nick Cave and the Bad Seeds - Papa Won’t Leave you Henry
“Man To Man”-Unknown Hinson
Unknown Hinson - Man To Man - YouTube
I’m a Boy - The Who
Arnold Layne (which I thought would be the second entry to this thread after Lola)
Cherry Lips by Garbage is a good example.
“Androgynous”-The Replacements
Yes, but:
*Sweet Loretta Martin thought she was a woman
But she was another man
*
https://www.youtube.com/watch?v=WDswiT87oo8
Blur - Girls and Boys
Looking for girls who are boys who do boys like they’re girls, etc etc
“Earache My Eye” by Cheech & Chong features these guest vocals by glam rocker “Alice Bowie”:
***My Daddy, he disowned me cause I wear my sister’s clothes.
He caught me in the bathroom with a pair of panty hose.
The basketball coach, he done kicked me off the team
For wearing high heel sneakers and acting like a queen.***
Tweeter and the Monkey Man by the Traveling Wilburys.
"Jan said to the Monkey Man, “I’m not fooled by Tweeter’s curl
I knew him long before he ever became a Jersey Girl”
Good response! Although I think it’s Sweet Loretta Modern.
there’s always This lovely little ditty by Nation of Islam leader Louis Farrakhan.
Weird Al’s “Truck Drivin’ Song.”
And I can’t believe no one has yet mentioned “The Lumberjack Song.”
The deliberately-offensive-in-every-way “A Lapdance is Always Better when the Stripper is Crying”, by the Bloodhound Gang, eventually reveals that the titular stripper is biologically male.
The lyrics I’ve found all say Martin.
From here: Get Back | The Beatles Wiki | Fandom
Deleted - Not relevant
Many (most?) of the other songs from the Hedwig musical/movie soundtrack, as well.
I bought the Blue Album about a hundred years ago, well almost 40 probably, and the liner note lyrics definitely said “modern.” Not that liner notes are always correct, and I can’t find an image on-line but that’s my story, and I’m sticking to it.