Right now a number of extensions treat JsConfigVars as a read-write store, reading a previous value of JsConfigVars, updating it, and then storing the updated value back. This is incompatible with the separate/asynchronous/incremental parsing model on the Parsoid roadmap, as well as with the "write-only" model of the Parsoid ContentMetadataCollector interface.
Replace the current ParserOutput methods for JsConfigVars with add and set variants, which are guaranteed to be write-only. set will throw an exception if a different value is stored for a key (although use as a flag where multiple places set the same value is permitted), and append will create an accumulator set.