All the previous stalker games could be run in centered window mode with the following command line argument: -center_screen, but when the same command line is used in call of pirpyat, the game won't launch at all, why, well because the game use a launcher named Stalker-COP.exe which is located in the main install directory, instead of the xrEngine.exe in the Bin folder like the previous stalker games. And just 5 minutes ago I fixed this problem and thought of sharing it here.
Now for example lets say your game install directory is C:\Games\S.T.A.L.K.E.R. - Call Of Pirpyat. Remember, I am using this install directory as an example only, yours might be different depending on which game version you use (steam, gog, retail) or if you chose to install in a custom directory like me.
1) Go to your game install directory and open the bin folder, right click xrEngine.exe and create shortcut on desktop
2) Open the shortcut's properties and in the target box add -center_screen at the end (remember to leave a space after the quotation " mark before adding any command line argument), so it should look like this "C:\Games\S.T.A.L.K.E.R. - Call Of Pirpyat\bin\xrEngine.exe" -center_screen
3) In the start in box, remove the \bin at the end so it should look like this now "D:\Games\S.T.A.L.K.E.R. - Call Of Pripyat"
and you are done, now you can play in centered window mode. Now you might be wondering why did I remove the bin from the start in box, well the game will give a 'Cannot open file 'fsgame.ltx. Check your working folder.' error if you don't. If anyone has any questions/confusions, please let me know.