Some extensions (like WikiData) currently set page properties using parser functions (using the setProperty method on ParserOutput). Those are not in the page content, nor are they exposed by Parsoid in any way.
We should probably extend the expandtemplates action (or whatever cleaner action we add) to return the serialized options array, so that this information is at least not lost any more.
Really a saner way would be to move this information into proper page properties in the longer term. Timo mentioned there was a bug for this, but I have not found this so far.