I also have the same issue, do you have any fresh information ?

After checking on real devices: iPhone on iOS17 and Apple Watch run-in watchOS 9, I confirm that App Store don't install the new version if both minimum OS requirements are not met. So it's handled perfectly well.

I also have the same question. It seems the migration is never called.

Yes ! And it's working perfectly !

I have exactly the same issue with a workout app and its iPhone companion app. HealthKit seems to be out of sync, it's like we have 2 different app reading and writing in 2 different HealthKit stores. I haven't found any documentation on that ...