I always got the impression that Gearbox hated GOG.
I don't know if they hate GOG, but they sure do like working with publishers that love regional pricing and regional restrictions. They also won't fix a bug in AC:M that causes it to crash on Japanese systems. All that is enough to tell me that them releasing on GOG is unlikely.
Further, seeing what they did with AC:M, would you even want a Homeworld remake they've had input on?