It seeems that I should have used 'jaxb' Bindings instead of 'jaxws' ones. Finally, I got wsimport working fine with this bindings file:
<jaxws:bindings
wsdlLocation="https://mutalyzer.nl/services/?wsdl"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
xmlns:jaxws="http://java.sun.com/xml/ns/jaxws"
xmlns:jaxb="http://java.sun.com/xml/ns/jaxb">
<jaxws:bindings node="wsdl:definitions/wsdl:types/xs:schema">
<jaxb:bindings node="//xs:complexType[@name='transcriptInfo']">
<jaxb:class name="TranscriptInfoByNM"/>
</jaxb:bindings>
<jaxb:bindings node="//xs:element[@name='transcriptInfo']">
<jaxb:class name="ElementTranscriptInfoByNM"/>
</jaxb:bindings>
</jaxws:bindings>