As long as the purpose and the use (at the most granular level) is specifically understood, the pursuit towards that type of metadata storage can be justified.
Remember the purpose of the metadata store – it was just to serve as a data dictionary in the simplest form. The ability to do something extra out of it was a by-product.
Your metadata repository structure does not have to be perfect, it just needs to serve its purpose. If you end up going down the path of making it absolutely right, then this is just over-engineering something simple.
Do NOT let the the metadata implementation & management overshadow the actual system implementation and your immediate goals.