Unfortunately I was not able to run this game in a window. I tried adding "-window", "-windowed", "-safe" etc to the target of the desk top shortcut and the launch options via steam.
I also had no luck when changing the number you specified. Every time I changed it the game reverted back to 800x600x32.
To get .set files with only the res altered I deleted the gta-sa.set file and launched the game. I changed only the resolution exited and cut/pasted the .set file to the desk top.
I did this with 800x600x32 and 1024x768x32. And I used the first instance these resolutions appeared in the game options.. Since they are listed twice in the video options I wanted to make it clear which ones I used.
I also did it twice with 1024x768x32 which resulted in different outcomes...which sort of threw me for a loop.
Results :
First let’s look at 800x600x32 and 1024x768x32.
800x600x32
1024x768x32
Now here are the two 1024x768x32...obtained with the exact same method. Only one change between the two...yet they are the same game settings.
1024x768x32 - The first one as seen above
1024x768x32 - The second one. You can see only one change.
I really do not know what to make of any of this.