When i set the option in "Default Setup" and try to Run the game (F5) doesnt scale the game, if i do it in winsetup it does scale the game.
That's because there is a user config for your game (edited by winsetup) that overrides values from Default Setup. Default Setup - this is what game uses only after it was installed on computer for the first time.
If you want to test how Default Setup works, go to "Saved Games" system folder (you can use "%USERPROFILE%\Saved Games" in windows explorer), find folder with the name of your game and delete acsetup.cfg there.
I was expecting that in window mode the game wouldn't be scaled, and would only scale in fullscreen mode, but again that is what I was expecting 
Well, in your case that would make sense, since you have 1280x720 game, but if the game is 320x200 not scaling its window would make it look very small, so games do have some scaling option applied most of time.
Maybe I could make it have separate scaling option for windowed and fullscreen, will it be convenient for players to set up?
By reading the previous posts I was wondering the same thing.
It would then be possible to have proportionally stretched fullscreen image and a maximum round multiplier windowed mode, for example.
This way, it would look "cleaner" in windowed mode while retaining a "real" fullscreen mode.
That might be possible to do... Not sure how well it look in winsetup; probably it will need to remember both scaling options and switch between them when you tick/untick the "Windowed" checkbox.
Indeed, sometimes, by stretching the windowed mode, you have some parts of the window hidden behind desktop elements (e.g. taskbar).
Hmm, I thought it takes taskbar into account when calculating max window size. Probably not working perfect all times.
