So I bought this game and now I wonder if there is a way to center the game to one of its native resolutions (640x480, 800x600 and perhaps 1024x768) instead of having it scratched. An ability to have it in windowed mode would be nice as well.

Yes, there should be way (long long time ago on windows 98 i had it once set windowed)
You would require to edit a file c:\users\<username>\My Documents\corsaiars.ini

But You will need to add something like windowed=1? i am 100% not sure what to add as i do not remember it being straight forward if gog team could let us know how i would be grateful too.

I was looking into that file before but there was nothing I could change to adjust the resolution.

I assume you want the game to be in the center screen, and not stretched across the entire screen? If you have Nvidia card, that is very easy thing to do. Go to your Nvidia Control Panel -> Adjust desktop size and position. Now select "Perform scaling on: GPU" and set "Select scaling mode: No scaling". Hit "Apply" and you are all set.

No need for windowed mode. Game will be reproduced in its native resolution without stretching.

I have ATI card with GPU scaling enabled and screen centring works for every single game I have as well as for Windows 7 but it fails to work with Corsairs.

You are right. For me it centers the game but within limits of aspect ratio, not all the way in the center. But then, I had a hard time just getting the game to finally run.

This is a notoriously hard game to get working. I doubt even GOG.com can introduce windowed mode.