Is it? I just installed the Origin version of this game as there is no patch installer outside of Origin.

Ran the game in 1920x1080, overlay is still broken.

All these people saying it works for them, I'd be interested to know whether they're running Nvidia or ATI

GOG has not done any work on the Origin version of the Game. GOG has done work on the GOG version of the game.
While it is possible that the Origin version will eventually be patched, the only currently patched version is GOG's.

I started playing the game, and the bug is not fixed. I changed resolution in the text file manually (config.ini), because I'm playing the game in Wine, and settings tool doesn't work in it. The map is still messed up during zooming.

My resolution is 1920 x 1200.

It works ok for me in 1920x1080 on WIndows 10 x64.

The game does not officially support Linux as far as I can tell, so perhaps it was not playtested with Wine and had specific issues with it.

Did you also set the resolution manually by editing the config.ini or did you use the "Saboteur Video Settings" config tool?
It seems that in my PC that tool doesn't have the option for 1920x1200, but that could be either because my monitor max resolution is 1920x1080 or that it's not supported by the game (or both).

Previous resolutions in the dropdown of the "Saboteur Video Settings" config tool include:
1680×1050 (this is 16:10, can you try this just to see if it works for you? )
1680×1024
1600× 900
1366x 768
1360x 768
1280x 1024
1280x 960
1280× 800
1280x 768
1280x 720
... (and a few lower ones)

I used the config tool - will give it a try on 1680x1050 to see if the bug is there, too

Otherwise I will play on 1920x1080 with small borders rather than having this damn map bug allover again after buying the GOG version (despite having it on Origin and somewhere on Disc)

Seems to be partially fixed for me. Icons and the grid displays properly, but zone overlays seem to still be bugged.
For example: red overlay zone when escaping from nazis.

Yep, unfortunately the zones aren't fixed. But still better than the original release version.

Can you please explain how it was fixed exactly? It's not working in Wine, and understanding what was done can help making it work in Wine as well.

Does anyone has an earlier GOG version without the fix? Comparing them can provide the info what exactly changed.