This is an issue that really can't be fixed imo.
If use the scheme "app/storage" then migration/deletion of singular apps is easy, but if you want to touch just a part of every program (e.g. delete the cache) then its filled with the same tedium you were initially complaining about with regards to uninstalling.
On the other hand, the scheme "storage/app" allows you to "nuke" the cache for every installed program without touching the config at all (while lessening the ease of complete removal).
As I don't usually remove programs (or install new ones, for that matter) the scheme that works best for me and many others is "storage/app". In an ideal world a hybrid scheme might be possible, but as it stands now it is not an option and one way has to be chosen over the other.