Does the Bayern ticket cover the Zugspitzebahn?
No, but it does get you a 10% discount. See here for all discounts with the Bayern-Ticket (in German). (It's the first entry.) The cog train from Grainau up and the Gondola are the Zugspitzbergbahn and are not covered by the Bayern-Ticket, only a discount. The train from Garmisch-Partenkirchen to Grainau is a regional train and is covered.