Your KDX axle fits the KX forks?
Not that I've ever found. You can have an axle made (you know...from your local CNC buddy down the street?) that will allow the KDX wheel to be used with a KX fork. That's been done.
The KDX caliper fits on the KX fork. The comment, ' (because the KX fork uses a different hole spacing for the mounting)' is curious. The brake line routing (banjo angle) is different, but the caliper itself is not.
The answer to your question (for whatever reasons you ask it): Center the rotor in/to the caliper.
Something to think about...if one pad was stationary, as the pads wore the 'center' of the pads would also move. That would work exceedingly poorly, 'eh! ;)
Good luck. Methinks you will need some!