Yep, 16 lanes will go to the PCIe and 20 to the PCH controller.
The bottom PCIe slot goes through the PCIe controller as does the M2 slot.
No issues with the M2 slot at all, its just either or with the U2 and who wants U2?
Here is a diagram of the architecture.
You cant do the top two slot and run SLI as the second slot is X4 Have to do the Top and 3rd and you get X8 on each.

As for performance hit, this should show you there are no worries. See specs for machine build on M8E.
M2

Firestike Ultra with 2x Srix GTX 1080 A8Gs in SLI using high bandwidth SLI bridge.

“Two things are infinite: the universe and human stupidity, I'm not sure about the former” ~ Albert Einstein