"Haki transcends all" doesn't translate to Haki is always supreme. It just means Haki has limitless potential unlike other abilities, which stop growing after a certain level regardless of the user's potential. This difference can only be observed at extreme levels i.e., at the top-tier level to be more specific.
You have Roger, Rayleigh, Oden, Mihawk, Shanks, Garp, etc, all of whom have no devil's fruit power but still made it to the top. But if you look at the devil's fruit users, even the most gifted users with the most overpowered abilities like Whitebeard, Luffy, Blackbeard, Kaido, Akainu, etc, need Haki to complement their capabilities to stand at the top alongside those mentioned earlier.