I have recently bought Fallout 4 and since I use Vortex for several other games, I took it for Fallout 4, too.
My problem is that actually it doesn't work at all.
I found out that Vortex put the mods to \AppData\Roaming\Vortex\fallout4\mods under C: while the game is installed under K: and even has an own mods folder. My attempt was to simply copy the content to \Fallout 4 GOTY\Mods but it seems it doesn't work either.
How are mods for Fallout 4 are actually managed to get them to work?

Edit: I fiddled with some settings and finally got it.

I changed the mod folder in Vortex to drive K: where Fallout 4 is located which made it possible to use the deploy mods command in Vortex. Using the folder \Fallout 4 GOTY\Mods wasn't possible so I had to create a folder outside the game files.

I'm using vortex too. I'd recently installed my GOG fallout 4 and played it a bit to make sure it works. Well when I went to find the saves, guess vortex takes all the saves to documents/my games/fallout 4. I found it placed those saves under the current profile I had enabled at the time for the Steam version of the game that is being managed by Vortex. I never changed the game management for Fallout 4 steam version...just installed the game on that drive and the saves go directly to my c drive in that folder.
I had changed the folder that has the mods under appdata file (owner) to the same drive as vortex and game is installed on which is the setting in vortex you can do...but there is no setting for moving the save folders to the drive the game is on which is E for me.
So what file did you create to get Vortex to install mods on your GOG version and manage it or did you change the hardlinks that go to the Gog install so it launches that instead of the steam one? This is very confusing but if you got it to work then can you tell us how that is if you had to make another link for your game? Is that how vortex works as in it has to think the game is a different game? So confusing. I'd like to move the saves folder to the E drive instead of my operating system but vortex has no settings for that so I'd probably need to make a virtual forwarding link for that.