duh, went back to the docs, to prevent gun from persisting to a json file when you already have level-up persistence, do this:

const levelDB = levelup(
      encode(
        leveldown(this.opts.file),
        { valueEncoding: 'json' }
      )
    );
    //both radisk and localStorage must be set to false
    this.db = new Gun({level: levelDB, radisk:false, localStorage:false, web: this.httpServer});

oddly both radisk and localStorage must be false, otherwise I get other errors like:
BUG WARNING: Radix Storage Engine (RSE) has a known rare edge case, if data gets split between file chunks, a GET may only return the first chunk!!!

You guys are welcome to close this, but I suggest we update the README with an explanation so others wont be persisting data to level and the standard json file at the same time.