Right now I am running GOG Galaxy in bottles and it is mostly stable. However, I don't like how GOG Galaxy constantly is showing ads and harvesting data.
What I am looking for is another Windows launcher that can manage GOG games. Ideally it should be simple and work with a controller.
I also need an alternative to the cloud sync. I think it might be possible to either use Syncthing to sync folders or to setup a network share and then use some scripting to save my progress once I'm done playing. The biggest issue I have is that I don't know how to import my GOG cloud saves into the offline installer.
I believe it's configurable whether you get notifications about new releases on Galaxy, just like how it is with steam. Although one thing I've noticed is that claiming free games on GOG will toggle the notifications on again so you need to turn it off after claiming anything.
Regarding cloud saves, Heroic will let you download or force download them. After that you would just need to place them where they are expected for the game.
I use Heroic on desktop and deck and am a big fan personally.
Native vs wine/proton locations will vary and even when emulating windows some games use "My Games", "My Documents", %APPDATA%, etc for the save file location.
Why tf are you using GOG Galaxy under Bottles when Lutris is better than Bottles in every single way and integrates directly with your GOG account, meaning you don't need GOG Galaxy at all? This is like pulling the handbrake on your car and pushing it uphill instead of turning it on and driving it, in terms of how needlessly difficult you're making things for yourself.
Related question - will any 3rd party launcher allow for multiplayer authentication? Right now I install each game manually but sometimes I want to play on online servers.