They are legally separate entities, but why should that affect customers?
Because they are not doing it because of customers, they are more likely doing it for themselves. It’s easier to manage things on a corporate level when the data is also separated similarly as their companies are.
My guess is that they just want to separate GOG and their game accounts from each other because they are easier to manage that way. I think in legal sense GOG is still a separate corporate entity even though it’s owned by CD Projekt.
I always found it kinda sad that Destiny has a lot of lore, but if you are a new player / returning player you can’t experience the lore that you have missed because it’s just removed from the game.