Hey @el, I've painted saddles a couple of times. Used a 100% acrylic paint, kind that comes in a tube. Rubbed it on with a rag. These were saddles that I had recovered with various types of vinyl from the fabric store. So not a stock production saddle covering.
The acrylic does wear off gradually over time. I never did try to seal that with a clear of any kind. But for a rat rod bike I didn't mind.
I also used Flex Seal on a couple saddles,yeah, the black stuff that seals and protects everything under the sun. I did spray that with a matte clear, and it held up well. Very durable.