Ok, this is what I was told at the store here. I did turn on the option to automatically select the Rewards card while at the store but didn't notice anything different than any other time. As stated here, the terminal is not waiting on me to scan a rewards card because EMV requires me to wait until the end. I did try to scan my rewards card at the end of the transaction but the terminal just said it was not a valid form of payment. We backed up the screen where a rewards card could be scanned, nothing happened via NFC so we scanned the barcode which gave me the points. I did pay with Apple Pay in the end. The cashier said they have no idea how the rewards card would combine with the payment card unless something changes because as it is now, you can't add the rewards card info until the end. So, maybe something will change and I just could not figure it out but as of today's test, its no different than it was last time I made a visit.
Edit: I just added my card to wallet again to see if anything was different. It asked if I wanted to select the card automatically, I said yes. I did this on the other card that was already in my wallet via a switch in the card info. Doubt this will make a different but thought I would add this detail.
Edit 2: found a link to an article on CNET showing the process they found. If you notice the terminal, it says "Please enter your phone number or tap your device". When I tried today I only had the option to enter a phone number. So, I think I was just a little early to the store I tried and yes, it does take two taps to complete the transaction. One for rewards, one for payment according to this link.
http://www.cnet.com/news/walgreens-first-to-link-loyalty-program-to-apple-pay/