In testing, adding fields to PMPro Member didn’t seem to have any effect on the Paid Memberships Pro fields or interface.
Tested with https://github.com/strangerstudios/paid-memberships-pro/ and PMPro Pods Add-on enabled.
I may be missing something as well; this might be a good question for the Paid Memberships Pro team as to what’s supposed to happen when extending those types.
Adding fields to Users will add them to the profile page in the WP Dashboard area.
You can extend the PMPro Member object and choose to show groups of fields on the PMPro Member Profile page, the WP Dashboard User Profile form, and/or on the PMPro Checkout form itself.
So it’s essentially covering some of the same ground as the User pod could but it has much more context it can work with from PMPro.