"I'm so baffled about how if you say males have penises and females have vaginas, that means trans people don't exist"
No it doesn't.
It means transwomen are male and transmen are female. Which is the literal truth, as per dictionary definitions that state:
Female: Of the sex that can make eggs or bear young.
Male: Of the sex that can make sperm.
"they clearly do because they are there. Laverne Cox and Caitlyn Jenner haven't disappeared in a puff of logic"
Logic is on our side in this, I'm afraid, not yours.
Caked-on makeup, facial surgery, and dresses have not made Jenner Of the sex that can make eggs or bear young. Jenner is still Of the sex that can make sperm, and is therefore male.