If there are so many clearance issues to use that cooler, it is definitely a good idea to return it and pick another solution, either a water cooler or another air cooler.
Nowadays indeed most motherboards have backplates to support the weight and also the tightening stress exerted by cpu coolers, but if you observe carefully, you could see that heavier cpu coolers can still bend the motherboards slightly. After knowing and seeing this, I have never installed any heavy air coolers in any of my motherboards any more. I simply upgrade them to water coolers that cost as same as some heavy and high end air coolers.
And if you don't plan to overclock too much, an average water cooler is already enough to cool the processor. I personally use three Corsair H55 water coolers on all of my systems that have a slightly overclocked 3770s, Xeon 1276v3, and another Core 2 Quad 9650 overclocked to 4GHz. All run fine for many years combined.