The Supermicro M2 PCI-E slots vary from board to board:
H11DSi: Qty 1 PCI-E 3.0 x2 lanes
H11SSL*: Qty 1 PCI-E 3.0 x4 lanes
H11SSW*: Qty 2 PCI-E 3.0 x2 lanes NOTE: 2 additional NVMe ports on H11SSL-NC model, plus a SAS RAID controller (and SATA as verified by SM)
New Server Specific Boards
H12SSW*: Qty 2 PCI-E 3.0 x2 lanes NOTE: Dual devices are switched x2 - Single device can run @ x4
H12DST*: Qty 1 PCI-E 3.0 x4 lanes
H12SST*: Qty 4 PCI-e 4.0 x4 lanes (sweet...)
Like others I do question why some of the boards only offer x2 lanes when so many lanes are available as I do not believe any of the above designs are totally maxed out on lane consumption. BUT the reality is, boards like the ATX HS11 series have 3 x16 slots and 3 x8 slots and offer bifurcation on all slots and with M2 PCI-E adapter cards you could have up to Qty 18 additional 4 lane M2 cards if you wanted...
With the additional NVMe ports and RAID controller, the H11SSL-NC would be my Supermicro board of choice. I don't have anything that requires PCI-E 4.0, but dang it's hard to invest in a new purchase with last gen tech....
The Gigabyte board is a great option if you want Qty 2 M2 PCI-E x4 lanes, 4 additional NVMe ports, or need the 16 memory slots and can utilize an Extended ATX board...