According to the manual page 33 or 34, if you install 3 NVMe PCIe x4 SSD's (SATA SSD's or x2 SSD's have different behaviors) then
M2C_32G will disable SATA port 4 and 5.
M2D_32G will disable SATA port 0, 1, 2, 3.
M2A_32G will not disable any SATA ports.
So you will only have SATA port 6 and 7 remaining.
None of the M2 slots affect the PCIe slots.