If I use the Ultra M.2 Socket (M2_1) at GEN 3 (PCIE x4) then will it take away PCIE lanes away from my graphics card (gtx 1080 ti)? I ask because I know this is what happens with the Asus Crosshair Hero VII x470 board.

Getting this information from "der8auer " from youtube who went into a full review of the Asus Hero VII

ASUS CROSSHAIR VII HERO - Everything You Need To Know! X470 In Depth Review (en) - YouTube

So will the same thing happen with the Taichi Ultimate? Using the M2_1 Slot will force my gtx 1080 ti into PCIE 3.0 @ x8 instead of x16?

I would just use the M2_2 slot but that only has Gen 2 speed instead of Gen 3