It's more that they want to try and convince people to pay with Walmart's own lower-cost (to them) app if you want to do contactless payments from your phone. If they made it easier to use Apple Pay, why would anyone ever use their app?
Why would paying with the Walmart app be lower cost to Walmart? Both the Walmart app and Apple Pay are essentially, as far as payments go, just digital wallets that you can store credit card information in.
When you use them it is still a charge to one of those credit cards.
It might actually cost Walmart more in my case, because the card I have on file has larger rewards for online purchases than it does for in-store purchases, and the Walmart app processes purchases as online even when made in-store. If I pay with the physical card it is processed as in-store.