According to wss.xsd from (12\Template\XML), ContentTypes also supports having ContentType element as a child, not only ContentTypeRef:
<xs:complexType name="ListMetaDataDefinition">
<xs:all>
...
<xs:element name="ContentTypes" type="ContentTypeReferences" minOccurs="0" maxOccurs="1" />
</xs:all>
</xs:complexType>
...
<xs:complexType name="ContentTypeReferences">
<xs:sequence>
<xs:choice minOccurs="0" maxOccurs="unbounded">
<xs:element name="ContentTypeRef" type="ContentTypeReference" />
<xs:element name="ContentType" type="ContentTypeDefinition" />
</xs:choice>
</xs:sequence>
</xs:complexType>