I am with Dimitris here.
What I see a deployment marker could do is be a visual indicator to the admin whether the given package is deployed (successfully or at all) or not while if you look just at the deploy dir in, e.g., AS5 you see only a list of deployments and you can't tell whether one of them failed w/o checking the logs or admin console.
And for exploaded deployments it solves the deploy-before-fully-copied issue.
But I would still prefer the traditional way if it were just for the advantages above.
Plus, as Jaikiran says, if the deployments are really substituted, what if you are unsure and want to check the exact deployment descriptors and resources deployed? How would you do that?