This is still on our radar, though we don't have much progress to report since the citation work you noted. The citation markup assistant was a big step in the direction of merging XML functionality into OJS, and we have several interested partners and one major grant awaiting a decision. We still consider a fully-automated translation from a layout format (.pdf, .doc) to a semantic format (NLM XML) to be beyond our current resources, but you might be interested in OxGarage
as an alternative project.
Public Knowledge Project Team