Bootloader unlock worked great, but flashing TWRP via this tool just resulted in the "No Command" message when attempting to entry recovery. Had to manually flash TWRP myself, and now can enter recovery.
Now the issue I'm having is that after trying to flash the SuperSU zip, I'm also stuck on the first Moto logo. Tried flashing SuperSU 2.46, but that didn't fix it. Also tried doing a factory reset via TWRP and wiping data, but no dice. What can I do? Help...
EDIT: Nevermind, did a full restore to stock. I think I'll not mess with root for a bit until systemless is more stable. I use Android Pay quite a bit, so I'd rather not screw around with trying to get standard root working right now anyway.
I had basically the same problems you had. I changed the TWRP img file WinDroid uses to the most recent one from their website to get recovery. I have links in this post 129
Then I used this method to get root.
[ROOT] Moto X Style - XT1572 BR - Marshmallow by ivcarlos
I did that last night. Worked like a dream. But I don't believe this will help you with the Android Pay issue.
Above notes and methods approved by @Ohmster and @OldBaldy. They were lots of help.
Good luck