Anyone in my circles that has a direct contact with someone from Shopify that could help us understand TOS around payment plugins?

It seems they've been written from a perspective of traditional payment gateways, but @BtcpayServer does not have fees, and is not an intermediary.

We are trying to put an app where BTCPay users can connect their BTCPay and accept payments directly

These requirements aren't future looking enough and don't take this case into consideration.