Like mrmoe110 touched on, above, having to re-enter your PIN / password a second time when any sort of Smart Lock is enabled is a security feature, methinks...
Let's say you have a smart watch set up as a Trusted Device, which allows you to bypass entering your PIN / password on your phone, as long as your watch is with you. In theory, somebody could steal both your phone and your watch, thus having unfettered access to your phone's contents. Having to enter your PIN / password a second time proves that you are you, when it comes to using Android pay to make purchases.
Same thing goes for Trusted Locations. Example: I have my workplace set up as a Trusted Location. We recently got new vending machines in the breakroom that accept NFC payments. Again, in theory, somebody could get a hold of my phone and go on a snack shopping spree, stocking up on Snickers and Mountain Dew - having to enter that PIN / password a second time prevents that from happening. I imagine this would also be the case for people who work at businesses that accept Android Pay / NFC (Panera, Walgreen's, etc), and have their workplace set up as a Trusted Location. Say they unknowingly drop their phone in the parking lot? Somebody could pick it up, walk inside, and shop away - again, that second PIN / password stops that.
-Phil