That PCIe breakdown is awful. The switching of the M.2 slot to PCIe 2.0 x2 from 3.0 x4 would be unacceptable; buying the NVMe PCIe 3.0 x4 SSDs today is a premium purchase and anyone interested in that simply requires that it runs at 3.0 x4 - not 2.0 x2 (a mere quarter of the bandwidth). The fact with a 40-lane CPU you can only get 3.0 x4 M.2 working with 1 or 2 PCie cards is absurd even for a $200 board. The fact that a RAID controller operating with an x8 configuration counts as well means that you can have an M.2 NVMe 3.0 x4 SSD, an x8 RAID controller, and be unable to run SLI graphics. Unless you buy the cheaper 28 lane CPU - then you can have SLI, RAID, and NVMe 3.0 x4.
The engineers who came up with this one probably were trying to get people who were considering the 5930K + $250 X99 board to consider the 5820K + $500 board - net cost is about the same, but clearly MSI would benefit more from the second purchase than the first.