Oceankhayne: It's possible to do this with Mod Organizer 2. I have it up and running and it works great. You can copy the contents of your Fallout 4 GOTY folder into a new folder in Mod Organizer 2 you create and name 'Stock Game'. If you set it up and then point your paths correctly then there's no issues. You just have to remember if you're running MO2 with the GOG copy of FO4 you have to put -forcesteamloader in the arguments field of f4se_loader.exe inside MO2. You can then use the MO2 root builder plugin and copy the contents you need into a new mod folder you prepare. Attached is what it can look like when you have it setup properly. The Fallout London and MO2 discords are your friend. Both have written guides as to what to do.
And you're right. Even if they couldn't distribute this software themselves due to rights issues, they could've worked on a video and text tutorial to help you set it up fully yourself.
I have my copy up and running just fine now and it runs great, but it needs all of those engine fixes to run as well as it does now.
The lack of such a proper step-by-step install instructions, for installing FOLON and keeping an existing install of GOG FO4 intact and playable, is why I won't be installing FOLON any time soon.
I don't want my install of GOG FO4 to be completely hosed by installing FOLON.