To be honest, Kongregate has a size restriction for their games, and I believe Stencyl should too. I'm not sure off the top of my head, but I think 800 wide is the max Kong will go.
Some of the sizes for these games are way too big. They are sizes better fit for a standalone game application. The default sizes that stencyl has, are the most frequently used sizes on any game portal, and I think a very large portion of our users, like 95%, will find these satisfactory.
Though, in regard to updating a game with a new size that is smaller than the previous, that would need to be fixed by someone else, unless there is an option in the edit page to change the size.