Is there a way to to keep gog saves and steam saves separate? I have both installed, and want to do something completely different with my gog modding setup. As is, my gog version wants to load all my steam saves, so they are sharing the same file structure.

Only thing I can think of is to use a mod manager that allows different setting and save locations under each profile. Vortex can do this, and another post has mentioned Mod Organizer 2 can also do this. When you install the mod manager and get it set up to manage the game, just create a new profile, and set the profile to manage separate settings and saves.

Things I do not know:

Whether each installation will be handled separately by the mod manager you use, or if there will be conflicts to resolve.
Whether you'll end up having to change profiles between each.

The reason I don't know these is because both the Steam and GOG versions point to the same default settings and save locations. It's possible that each executable will then just follow the same profile, then run into trouble because each has different mods under them.

Frankly, it's probably better to just get a mod manager and use the profile system to do exactly what you're looking for. I know Vortex saves the mods in one location separate from the Fallout folder, and then adds symlinks into the Data folder to link to the mod files you activate. Profiles can be used to have different sets activated, and changing profiles takes just a few seconds each time, as long as Vortex saves your mods on the same drive volume, so that it can use those symlinks.

Maybe you could try to setup an additional Windows user to have a different set of "My Documents" folders and the like.

You could even have more than one GOG install that way!

Actually . . . didn't even think about that. Bonus . . . won't even need multiple GOG installs! Unless you later want to run multiple versions of the main game. Even if you're managing mods manually, each Windows profile, because they're using a different settings file, will also have different sets of mods activated.

I use Mod Manager 2 and keep even character saves and mods per playtrough loaded separately. This way I have absolutely no game saves in the default location.

Use a mod manager like Vortex or Mod Organizer 2 to create different PROFILES for different characters,mods,saves and everything else. That is your best option for doing this.You can have different instances on MO2 to manager the different versions of the game aka steam vs gog for example. Only thing you have to worry about is that you have to manually install F4SE into the gog version instead of relyiong on the mon manager to install it for you. OTher then that you can use the mod manager to handle everythhing else

I like this idea. My steam fo4 is at least 6 years old, has like 600 manually installed mods, and is extremely stable, and would take a long time to recreate, and I love it.
But, I have a lot of ideas I would love to try, so the gog version/new windows profile is a no brainer.
Thank you for the tip.

Like others have suggested, I've been using Mod Manager 2 to keep them seperate. I let the Steam version keep the default saves in My Games directory in My Documents and have Mod Manager 2 handle GOG's version, as the GOG version also doesn't have the limitations with mods as the Steam version does.

FYI, in case you weren't aware, the Steam version disables achievements if mods are enabled. (That is unless you patch the game...)