I have purchased this version and realized that it is not fully functional like the Steam version. This one runs badly, caused by something about the engine.exe
When I replace the games engine file with the steam version, it runs fine.

It appears that the steam version somehow runs on more graphical memory. Also it does not output too much into the log.txt file, which might speed up game performance.

Attached is a screenshot of a comparison between the two log files after launching each game into skirmish mode. It seems like the Steam version writes a lot less output to the log file and maybe something in the GOG version is referenced incorrectly. The GOG log file writes the warning messages near the end about 20 times per second.

Edit:
System: Windows 10 64bit Pro
This only seems to affect Battle for Europe version of the game, not Napoleonic Wars. Added a screenshot from the log output for Napoleonic Wars comparison. Seems like performance related settings are identical and the NW version works fine. So something seems to be missing and cannot be loaded properly it seems.