Just an update on this in case anyone’s interested, or has similar issues.
Tried with a couple of wheels, and remounted the old caliper to check – the rear disk flatmount is definitely misaligned.
I noticed a couple of other older forum posts with people having the same issue, so this does seem to be Planet X “quirk”. I did reach out to them (was still just within warranty), and they were supremely uninterested. Didn’t push it as I can’t really stand the thought of being without my bike for however long it would take to post and sort out anyway
Current plan is to add a washer to the non drive side of the hub to push the chainstay out just a little (1mm)…hoping this won’t have a noticable effect on ride/balance?