GOG buys rights to distribute the original works for pennies on the dollar, the exemption EFF got is that you are allowed to reverse engineer and distribute software which can be used to run games that you own for systems that are no longer available, as well as transfer the games from their original media to modern ones in order to preserve them.
It doesn't not however give people the license to sell those games commercially doesn't matter if they are "abandonware" or not.
The only thing that comes to my mind is that now it may make commercial sense for GOG to ask publishers for rights to sell games that require activation systems / servers that are no longer maintained.
But if you're selling it with the blessing of the owner, what was stopping you from asking "oh, we also need to patch the game so it will run - I assume you don't mind?"
For GOG to sell a game at all already requires that they explicitly cut a deal with the game owner. Fixing the game to run on a modern computer is a trivial part of that deal (and something they already do with their whole inventory).
It could however mean that GOG doesn't need any terms for how to achieve it, allowing them to have patches created and updated for use on arbitary systems without asking for permission, once they already have permission for redistribution.
So if they got permission to sell a version that can run on Windows, then they could later on patch it to make it run on Linux and other systems as well.
It doesn't not however give people the license to sell those games commercially doesn't matter if they are "abandonware" or not.