I also own the Witcher 3 on GOG. I just checked the Steam Store page and they have the words "This content requires the base game Witcher 3 on Steam in order to play" highlighted in purple.
Just out of curiosity I added it to my cart and tried to check out. When I got to the last part before confirming my payment method I got this message.
"Your transaction failed because you are trying to buy 'Witcher 3: Wild Hunt - Expansion Pass' which requires ownership of 'The Witcher® 3: Wild Hunt'. Please correct the error and try again."
That being said The Witcher 3 is a DRM free game. If you are able to download the files from Steam I'm not sure why they couldn't be used with the GOG version of the game as long as you install them to the...