I think the first major difference would be if the budget is actually coinciding with the main estimates, you wouldn't necessarily see those sunset issues. If a program is being renewed within the budget, it would necessarily show up within the appropriation bill. You wouldn't necessarily have this potentially misleading indication that somehow there's money being taken out of a department or from a program, because it's actually ongoing. It's simply a timing issue in terms of how it's actually presented.
On February 29th, 2012. See this statement in context.