The first, possibly most serious, limitation originates in the fact that a standard DTD is severely restricted in the semantic dependencies it can express between two subtrees in the document structure.
if in the description of a contact, a city of residence is included, one may want to constrain such an information depending on the country of residence; or, in the aircraft maintenance manual example, one might want to automatically include some warning in case a dangerous chemical is mentioned somewhere else in the document.