Just wanted to post this here, in case someone else is looking for a solution to this.
I have a custom built ITX PC running SteamOS and a Steam Controller (Steam Controller Puck plugged into a usb-2 port on the back of the machine).
I wanted to wake the PC from sleep by just waking the controller, as you do on a console or the official Steam Machine.
On my AsRock B550M-ITX/ac I had to enable the following option in the UEFI Setup utility:
Advanced/AMD CBS/Chipset Common Options/USB Configuration Options/USB BT Remote Wakeup
After that it works perfectly, fast boot is disabled and I have my XMP profile loaded, but besides that all other settings are stock.
By the way, putting the console to sleep while a game is running works incredibly well under SteamOS (possibly linux in general, not sure). I love this feature and I can go back to gaming in single player games in literal seconds after a break.
If other people with Steam Controllers have motherboards from different vendors, and find a similar option that works for them, feel free to post it here.
Or if someone finds a setting or workaround to actually boot the PC when the controller is woken up, that would be even cooler, but not really necessary for me.