With a Z170 board my config as follows
CSM disabled
No changes to secure boot default
Raid enabled, M2 raid disabled, SATA raid enabled, PCIE4 raid disabled
No issues running M2 960 pro as boot device and 2x 1TB 850 EVOs in raid 0.
X99E is discontinued with the USB 3.1 version replacing it.
Looking at the boards architecture the M2 and SATA express share a common PCIe bus and it clearly states "OR"
“Two things are infinite: the universe and human stupidity, I'm not sure about the former” ~ Albert Einstein