> `MetadataStore`

Do you mean register a global `METADATA_STORE_BEAN_NAME` by provided **type** from properties?
Sounds good

> we'd only be able to load well-known properties that way.

That's why I suggested to have our own `Environment`, as it is in Reactor or Hibernate.
This way independently of provided resources from end-user we can allow access only for well-known properties. However why don't allow end-users to have their own properties with bean `INTEGRATION_PROPERTIES_BEAN_NAME`? 
We provide a strategy and, of course, the framework relies only on well-known properties, all others are up to end-user. Maybe he wanst to have a one place for his Integration Properties. Why not ?