Flash in stock 6.0 firmware;
boot into fastboot mode and load TWRP (3.0.2) with /system READ ONLY mode. I think this is the cause for the failure;
Install SuperSU (2.7.9-SR3). And saw a message "System-less mode. Boot image support required." on terminal. What does "boot image support reqiured" means?
Reboot and SuperSU works like a charm.
Update: I've tried to boot TWRP without /system write protection and flash in SuperSU 2.79-SR3 successfully. So only the SuperSU is responsible for this issue?
Which version of Magisk do you use? Magisk 7.0 (I think) was not compatible with SuperSU, as it has phh superuser included and disabled SuperSU. I would recommand looking for the Magisk version that is compatible with SuperSU. In addition, SUhide can also make Android Pay work, you can try that out