The backplate will be loose, and the stand offs don't screw flush. However when you put the pump block over the CPU and fasten it down it pulls everything tight.
What you need to do.
1) Find a way to push the backplate flush, you can use tape a spare hand, or of its already in your case stick something under it when you put the case on it side.
2) Make sure the protective film is over the water block
3) Get someone to hold the radiator or loosely screw it in to your case
4) Fit the pump over the block, screw the thumb screws in so its tight
5) Stand your case up and see if there is any play or movement in the back plate
6) If that is all good then take the pump off, remove the film and stick mount it fully with the thermal paste.
I'd suggest mounting it in the case, as screwing down your motherboard once you have the cooler and radiator attached will be a fun game. Just make sure your power cables are plugged in before you mount anything.
Looking at your motherboard, looks same as mine just shorter, so the above instructions should work. Let me know how you get on.