...Assuming we're talking cooling per individual system, with room to grow down the line for one or more w-cooled and oc'ed GPU/s per system, cooling performance-wise, there shouldn't be much difference between 2x 560s and the MO-RA3. Personally, I would lean towards the MO-RA3 because a.) a bit less less "plumbing" to do and b.) the option to use quieter 4x 200mm fans (push) or even 8x 200mm fans (push + pull). Also, per vid comment below by Gamers Nexus, apparently, the Mo-RA3 can 'passively' cool up to 200w
What speaks for the 2x 560mm option is if you choose to run dual loops (CPU separate from GPU/s) down the line in any of the systems. That is what I usually do when building oc'ed, multi-GPU systems (ie like the one in my sig) though there are pros and cons with both single/unified vs separate loops. Two 560mm rads might also be easier to re-deploy in future builds.
I'm not 100% certain yet about final configs, but my next build project will likely utilize two MO-RA3s 'in the back', with 200mm fans.