It's just a comfort thing really. Set the margins to 0 and you'll see it's really cramped scrolling around the layout, so it's nice to have some extra scroll space. In Classic the ability to change the margin was requested several times so I added an option for it - I guess people just like to change it according to taste.
The area outside the layout is useful for stowing away objects you want to place but not have in the actual game. For example, most of your bullets probably use the 'destroy outside layout' behavior. So you can have a row of your bullet objects outside the layout which will all be destroyed on startup because they're outside the layout, but it still gives you a place in the layout view to select them and edit their properties.