Part of this is (I think) coming from people being unfamiliar/uncomfortable with the default way that MC stores metadata. It can certainly be changed, but maybe the options to do so are buried a bit deeper than some people would like.
In a perfect world, we all wouldn't care about where metadata gets stored, just let MC and its internal database take care of things.
In the real world, people often like to see common-sense relationships like having metadata stored in the same directory as the programming material.
Maybe it's time to let the user tell MC to use its default, well-defined, well-functioning internal structure for metadata storage **or* let the users select another option that would cluster program material in the same directory as related metadata.
Allowing too many options here would be a programming, performance, and troubleshooting/reliability nightmare. But perhaps there is room for two sets of schema instead of the one we all pretty much use.
(This discussion might be pushing open the door to a re-jigging/rationalization of MC menu setup items too.)