His observation that ontological modeling alone is insufficient for syntactic disambiguation is spot on. The solution for semantic interoperability will combine ontological representations to model the relationships between data sources and a repository of transformation rules. What shape those rules will take is an topic in the research community.
Some folks at the University of Bremen published one such approach that combines ontological modeling with rule based transformations of syntactic elements. One of their conclusions is that rule-based transformations may be insufficient. They demonstrate classification transformation using traditional logic reasoning to deal with more complex transformations. They identify as an open issue the integration of these strategies to provide a comprehensive solution.
There was some applied work done by Robert Worden a few years ago on MDL or Meaning Definition Language. MDL attempts to define mappings between XML documents at a semantic level. Professional XML Metadata has a chapter dedicated to MDL where Worden demonstrates semantic interop between (IIRC) 13 different Purchase Order Schemas. XSLT is providing the transformation capabilities, while MDL models the relationships. MDL seems to be incarnated in a commercial offering from Charteris and renamed to Mapping Definition Language.
I would suspect that over time toolkits will emerge that will provide the building blocks for semantically sensitive syntactic transformations. Until then we are awash in a sea of bits.