Can't enable Apple Pay because another user already has it in use

I did eventually get it working after trying three different things, though I'm not 100% sure whether the combination is what solved it. It does seem like that "in use" message may have been misleading, however. What I did:

1. Although the other user didn't have Apple Pay set up, I logged out of that user's Apple ID.
2. Deleted all cards in the problematic Apple Pay user.
3. Turned off "Install system data files and security updates", rebooted, and turned it back on

At that point I was able to add cards normally. I actually suspect that the error message was a red herring and that it was the additional reboot step in #3 that got it working, but in any case it does finally work again.

A possibly relevant aside, which goes along with your comment, is that after first restoring my Apple ID was giving an error and told me to re-authenticate because of unspecified account issues. This initially didn't work either, until I rebooted and tried a couple more times. It's presumably connected to whatever back-end security thing gets munged up when restoring.

When you mentioned the "two different users" thing, it made me briefly wonder if it has to do with the User ID numbers changing after a restore, although the OS shouldn't be sensitive to that.

I'm not sure about the attachment to a system drive you mention, but the "hidden ID number" (or at least the one I was talking about) is the Unix ID of the user. You can view it by going to the Users & Groups system pref, authenticating, right-clicking on either the user that you're logged in as or another user that's not logged in, and selecting "Advanced Options..."

The "User ID" is a unique identifier for the user that's created sequentially, so depending on whether any accounts were created first, or what order they were imported in, these IDs are likely to change even if the users are the same on a migrated system.

That said, these days it's exceptionally rare for anything to rely on those IDs. I remember issues years back with an app that created hidden temp folders using the User ID number, which caused problems on shared drives since the user's ID would change depending on the computer being used, but because of under-the-hood changes in the recommended MacOS security structure I haven't seen a problem like that in a long time.

I assume whatever is going on here is caused by something else, especially since it was resolved (in my case) by disabling that auto-update, rebooting, and re-enabling it. It's probably as simple as whatever the Apple Pay security system seeing a hidden flag somewhere about which user is using Apple Pay, but after a migration that flag gets imported and no longer points to the correct user (or any user).