If you use the proper primer and paint that will adhere to rubber then yes Flex Seal can be painted over.
Anything can be painted over as long as you properly prime it and prepare the surface before painting it and then the paint will adhere to the Flex Seal.
I've painted over Flex Seal using some plastic paint primer first and then painted over the primer and Flex Seal with the proper paint and it never peeled off.
So as long as you prep the surface properly Flex Seal can be painted over.