Yes, it can be run in windowed mode. Run AGESetting.exe and set windowed mode and choose with or without window borders.
I would suggest using without borders, because with borders it is problematic to move the pointer to outside the window, without forcing the map to scroll, because when the pointer is over a border, it still causes scrolling. But by all means, try out what works best for you.
Also, if the window size you choose is equal to or greater than either of your monitor's native resolution measurements, the game window will be larger than that and one border or the other will always be out of view, along with a small stripe of the map. This is because the window size you choose is the playing area and not the actual window itself.
EG the native resolution of your monitor is 1024x786. If the window size you choose uses height 786, the game window itself will be greater than 786. When you put the top edge of the game at the top edge of your monitor, the map will extend beyond the lower edge of your monitor, which can make some things difficult to do in the game.
One thing you can do though, is to edit Display.opt manually to implement a non-standard window resolution. Try to pick a standard width though, because using a strange width can mess with the way the Stack Panel etc displays and works.