Im not sure about the support of low profile coolers for AMD. I have a HTPC using NH-L12S on AMD in a Silverstone ML04, and very confident Noctua has another model ready for AMD. A friend of mine building a mini itx is using one from Cryorig.
This is really smart. It would be good if all of them did that on all mobos. Things like that should be standardized as much as possible. It's kind of stupid to have to buy another cooler or water block to fit if you make a change like CPU brand. Really no different than mobo form factors like ATX and mATX.