Yes the M.2 SSD slot will work with 2 graphics card in sli/crossfire (I have tried putting my 1070 in the 2nd slot to test it, as I may add an extra card for SLI later on if I get a 4k screen). Indeed the mounted M.2 drive is slightly below the height of the PCH cover which sits underneath the 1st graphic card.
The point about it being blocked is that if you do have 2 graphics installed, the 2nd graphic card will block ACCESS to the M.2 drive. Meaning that if you want to swap out the M.2 SSD, you will need to remove the 2nd graphics card first before you can reach it.
Do note that the faster PCIe x4 M.2 SSDs (e.g. Kingston HyperX, Samsung PM951 or 950 PRO) do have a tendency to generate a lot of heat, and some have mentioned to add a heatsink to the SSD to reduce throttling. However this could make the SSD too thick and may have issues with the 2nd graphics card. Indeed the 2nd graphics card will also make it harder to cool down the SSD, but if you are using M.2 SATA drives the thermal issue should be less.
Side note: I have an msata crucial mx100 256GB SSD on my laptop and the Samsung 950 PRO 256GB on my desktop. For day to day tasks, I cannot tell the difference…so if you are going with this board and considering SLI, I suggest either using a 2.5” SATA SSD, or an M.2 SATA SSD. The board has U.2 connections also but there’s only the one Intel drive and it’s still quite expensive for now.