It was my vain hope to be able play the two versions, with very different set ups. At this time it appears that they will not work with both installed on the same pc.
Any ideas or work arounds yet?

They use the same location for the saves and .ini's
Not sure if that can be fixed though.

Use a Mod Manager like Mod Orginizer 2 to create different instances and thus profiles for the 2 different games. JUST A heads up you have to install F4SE manually into the game folder ont he GOG version for it to work correctly.

It's potentially possible with enough trickery to get one of the Mod Loaders to do it, but it's a pain because the location for .ini files and savegames is the same.

A much easier solution might be to install it on a seperate user account, which will completely separate the save folders. you'll want to launch from the Fallout4.exe (or the F4SE copy in the same folder) still to avoid any issues with the "launcher" pointing to the steam version because of registry entries created by steam.

It's possible.
I'm using Mod Organizer 2 with both GOG and Steam versions installed.