Bestop made the factory tops, so a Replace-A-Top would be a direct replacement.
My buddy with a TJ switched from a factory top to a Supertop from a factory style top and loves not having to deal with door surrounds although it is a bit draftier.
I used a Supertop on my old YJ and have one now on my CJ. Love them. Easy to put up and down. Have to stand on bumper with the lift though!
Than again, a lot of people rave about the Sailcloth Replace-A-Tops. Quieter, warmer.
Next time, post in the TJ Technical Forum please.