They provide 15 minute windows to complete transactions even though everyone in the history of BTC knows that 6 confirmations are the standards from the Blockchain. They use this to their advantage to sit on the BTC that confirms outside the 15 minute window.
I haven't used BitPay a lot and I've never used it from the merchant side, but from the buyers side, BitPay normally marks my low-value orders as paid a couple of seconds after I push send on my wallet. They do not wait 6 confirms. I believe once they see an unconfirmed tx with the right amount of fees they ensure its properly broadcasted across the network and take the small risk of a double spend.