It seems to me that if a seller uses square for transactions on their own domain that Afterpay should be available for customers on that site. I use squarespace as well. But it makes no sense that it's not available. It would benefit both Afterpay and Square as it creates another revenue stream
I have had this same issue, and the only way around it is to get in touch with Afterpay (which I have found to be harder than it should be) and to request approval from then. IN my case, needing to download another plugin (afterpay) and get that setup.
I am still waiting to hear back from Aferpay for the 3rd week after 3 inquiries
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