Usually the wake up from usb allows a system that is NOT powered off, to come back to life from a suspended state like hibernate or S3 etc...
Depending on the bios implementation and motherboard it may or may not be there to turn off or on.
Check with the vendor of your pc, or motheboard OEM.
Depending on what you want would determine to accept the default action or to change etc..
What I specifically was talking to was with a PC , a desktop in particular that is a DIY system i put together a few yrs old that even when powered off I see lights still on the system.
These only go off if I unplug the desktop from the ac outlet.
Its nothing to do with the USB wake up 'feature'...in my case...the usb port has 5vdc there but no wake up.
Aint technology wonderful.....I always shut down my systems when i am not using them...dont want them online 24/7.
Alex