But the downhills on a zero net elevation loop can never make up the time lost on uphills, not without putting out greater power. So your total time will always be greater on a 20 mile hilly ride than it would be on a 20 mile flat ride, given the same power, and your average speed lower. Maybe you're more disciplined on your hilly ride, and don't waste power for example.

Back to OP, I can understand wanting to include stopped time because the effort with a lot of resting isn't really the same as when you never stop. But the time you're waiting at a light doesn't say anything about your moving speed either - so I can't think of one as "better" or more accurate than the other. Just two different metrics.