Yep. 4-6 confirmations are what exchanges wait for when transferring millions of dollars. Who gives a shit when it's a $1 coffee?
Yup, when its the one dollar coffee, the merchant just needs to make sure a miners fee was sent. Otherwise the payment may be sent back to the originating address.
Confirmations don't really matter if there is a miners fee sent, speaking on behalf of small transactions.
Bitpay or another payment processor should offer merchants a credit account and/or insurance to provide instant transaction times, and make whatever adjustments might be necessary once the transaction is confirmed.