This was always the case with the Shopify App Store. They were more loose in using other payment systems, as long as you payed them their 20% by wire transfer. Since end of 2019 they give that permission to almost nobody.

It is also a big piece of the verification process for the App Store. So maybe you added Stripe later and now they found it?

Did you have a written waiver that you could charge another way? That is required at least since ~2015.