There is no need to worry about the M.2 compatibility list, any M.2 SSD should work in the Z97 Extreme 6, and you can boot an OS from that SSD fine.
Actually this board is the only one currently that would allow you to boot from the Samsung XP941 M.2 SSD, which has a special requirement that this board meets, without going into those details.
This board has two M.2 interfaces, the standard M.2 and the Ultra M.2. Any potential interference with anything else depends upon which one you use.
Neither M.2 connection will interfere with any other SATA drives or DVD/Blue Ray drives.
The standard M.2 interface uses the PCIe 2.0 lanes from the Z97 chipset that are specifically allocated to that M.2 connection only, so that won't interfere with anything else.
The Ultra M.2 interface will use up to four PCIe 3.0 lanes provided by the CPU (16 total) if an x4 M.2 SSD is connected to that port. The PCIe 3.0 lanes are used for the video card slots, so it would reduce the lanes available if two video cards are used, from x8/x8 to x8/x4 on the PCIE2 and PCIE4 slots. An x2 M.2 SSD would only used two lanes, so the result would be x8/x6.
The only M.2 SSD that currently uses four (x4) PCIe lanes is the Samsung XP941, all the others use two (x2) PCIe lanes. Currently, no M.2 SSDs can use PCIe 3.0 speeds, they all operated at PCIe 2.0 speeds.