The first one applies on both normal disc channel and usb/cfg/wiiflow loader because you'll still need have a connected jumpdrive even if you're using an original gamecube retail disc.
The second one was to avoid using usb/cfg/wiiflow loader altogether and use gamecube retail discs on disc channel with Padhook enabled.
The second one was to avoid using usb/cfg/wiiflow loader altogether and use gamecube retail discs on disc channel with Padhook enabled.