Register Apple Pay domain to multiple developer teams

Apple's docs state: "You cannot register the same domain with a different Team ID."

Right.

Regarding:

I don't know how Stripe implements Apple Pay or what their developer setup looks like

I'm not sure either, but I'm guessing that they may be acting as the Payment Processor where they registered the domain and maintained the Payment Processing Certificate. This can be done by a Payment Processor for multiple Merchants.

Regarding:

Assuming they have a developer team ID, I'm wondering if I need to unregister all the domains currently registered via Stripe so that I can re-register them to my personal Apple merchant ID.

Essentially yes. You will need to get into contact with Stripe about this and arrange to transfer the domain to your Developer account. Now, keep in mind that you will still need a Payment Processor, so I'm not sure if that will still be Stripe or another entity.

Matt Eaton
DTS Engineering, CoreOS
meaton3@apple.com

I went ahead and tried this with our sandbox Apple Merchant ID and was able to successfully register the same domain to our account that was registered via Stripe. By "successful" I mean that the register merchant API returned a 200, and I was then able to see that domain via the get merchant details API.

Okay, so you were able to get the same domain registered to a diferent Merchant ID, but still under the same account. The next step is that I would try a test payment in the Sandbox testing environment here. If that goes through then you should also configured a production payment in coordination with Stripe.

Matt Eaton
DTS Engineering, CoreOS
meaton3@apple.com