We just released NServiceBus.RavenDB 6.1 which provides a new overload when configuring the document store with access to the IBuilder. This should let you allow resolving the document store from the container and the this factory is only invoked at the actual endpoint startup time. You can read more about this API on the docs here: Connection Options • RavenDB Persistence • Particular Docs.
Please let us know whether that helps.