A content type's entry in the portal_types tool has 3 properties related to where the model is loaded from. They are checked in this order:
- model_source: The XML model, inline
- model_file: Path to a file which contains the XML model
- schema: Dotted path to a Python schema
My guess is that you need to make your filesystem product's installation profile explicitly empty model_source, so that it won't take precedence over model_file and schema.