These days I wouldn't be surprised if fairly large portion of XML documents that are still in use/produced did have multiple schemas. Most of the simple use cases have already moved to JSON or similar formats.

One very common case where there are multiple schemas is SAML. SAML protocol responses have their own schema, SAML assertions have their own schema, assertions usually define their type with different schema (XML schema instance) & XML signatures have their own schema. https://www.samltool.com/generic_sso_res.php for example