The Breeze documentation says:
This [MetadataStore.FetchMetadata] call is made automatically by Breeze just before it attempts to perform
I've submitted this bug for Breeze, which addresses this issue:
$metadata handling: entity types in separate schema from container not supported #96
I don't think it's correct that Breeze requires the EntityType namespace to match the Schema namespace - I think it's a bug.
The fix is a 1 line fix, which you can find here: https://github.com/johncrim/breeze.js/commit/9caa76a0de903e08083f600a2a23b9203ef87b49
You can use https://github.com/johncrim/breeze.js if you like, it only includes that patch on top of the current breeze.js master. But note that it's already 4 commits behind Breeze:master.