One way is to use a life cycle class (see http://www.vogella.com/articles/Eclipse4LifeCycle/article.html ). The application model is available at the point the @ProcessAdditions
annotation is processed so you can find your top level window and set its size there.
@ProcessAdditions
void processAdditions(MApplication app, EModelService modelService)
{
MTrimmedWindow window = (MTrimmedWindow)modelService.find("window id", app);
// Can call window.setX, setY, setWidth, setHeight here
}