Correct, diverting via the Queensferry Crossing omits the 2 stops either end of the Forth Road Bridge
Probably also because there's a limited market for the Panther LEs. The mix of the stop-start nature of the Dunfermline/Rosyth end of the route and the express Ferrytoll - Edinburgh section, combined with a short overall end-to-end journey time (not requiring a toilet, extensive luggage space, etc.), makes them ideal for the X55. Stagecoach would probably find it difficult to displace or even sell them if they introduced a double deck fleet on the route