Wanted to start running WW. I actually have the disc but I don't want to risk scratching it in any way. So: Is a GC modded with Picoboot and Swiss considered emulation or is it legit for runs?

Anything beyond booting the game through the disc channel or booting a disc through an allowed loader like neogamma /swiss, is considered emulation. Launching an iso on console, playing disc through ninendont, or playing on emulator is classified as emulator. Do note that we do have thresholds per category that allow emulator classified runs up to a certain time threshold.