I would argue, I think most systems have more quantity and churn of applications than users. Meaning, it would be better to pay some overhead to deal with "use

I would argue, I think most systems have more quantity and churn of applications than users. Meaning, it would be better to pay some overhead to deal with "user's crap" in every application bundle than to deal with "application crap" in every user's home. Your second paragraph though is probably closer to a realistic solution. That is, the OS provisions an Application Support directory and restricts the application to using it exclusively. Any application uninstalls can (via admin prompting or configuration settings) then also delete the support directories as well.