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I had the same problem with NVN2 on Win 11 with a 4K monitor. The game ran only in 1024x768. Changing settings resulted in either a complete black screen or a small black window with a flickering mouse. That included changing the setting in the game, launching in windowed mode using a launch parameter (in GOG Galaxy or direct) or editing the .ini.

Finally only one thing fixed it. Launch normally. When it is in low res full screen use Alt + Enter to force it into a window. This window is of course 1024x768. But then you can edit in the game settings to any resolution and the window grows appropriately. Now I have it running in 1920x1200 on my 4K 3840x2160 monitor. And it launches into the mode. Unfortunately this does not work on all of these old games but it worked on NVN2.