What aren't you seeing? Let's take Walmart as an example.
They don't want people using ApplePay because it costs them a small transaction fee. If their shoppers use WalmartPay, they benefit two ways. One, they save the transaction fee and can either keep it or give a little back to the shopper. Secondly, they get to keep all of the customer's data.
The small throughput increase by having the checkout process happen 3 seconds faster is negated by the monetary benefit. I'm sure they've done the math and chose the option that makes them more money.
Also, if you've ever been in a Walmart, it seems they care very little about speeding up checkout times. Just about every time I've been there, they have about 4 lanes open with a dozen shoppers in each lane, but they won't open up a few more lanes. Surely they've done the math and it shows that their shoppers don't care as much about checkout times than they do about the low prices.
Other merchants have their reasons as well. But it all boils down to money.