It’s not clear why the two versions differ in this way. When asked for comment, developer Mediatonic said, “We’re currently looking into this and hoping to have it resolved in a future hotfix.”
On a serious level, the ability to rebind buttons as a whole is a key element of accessibility for many players with reduced mobility in their hands.
On a less important level, for a fully controller-based version of a game to not offer any customisation (when it exists on other platforms) is, well, just a bit odd. It may seem a minor issue, but for the sizeable number of absolute brain-geniuses like me who prefer their Y-axis flipped, it will make the game meaningfully more difficult to play until the option is added.
Hopefully, it won’t take too long for Mediatonic to remedy the issue.