XSD has the target namespace, do we also need to modify the existing app.config

We want to have  a separate .xsd(schema files) for my two libraries, but with this approach, there will be conflict issue due to the same enum definition exists in BOTH .xsd files.
To resolve this issue, by adding the attribute targetNamespace into the schema element in the XSD file.

But what we have observed is with this approach  we might need to modify our App.config to specify the namespace to be used.

but we need a solution that will NOT require any modification to app.config file, especially if there are existing applications that use this app.config?