In my understanding it should be possible as you have till Basel your Swiss GA and from there the German Railpass :)

Bestway to confirm is you visit a SBB ticket office (you can buy even the reservation directly there) or you ask Austrian Rail as operator of the Couchette and Sleepers on this Route and book then the reservation on their website oebb.at 
For the seating car´s it works for sure as these Car operate as usual “Intercity”

This should not be a problem. I've often used night trains from/to Switzerland with a similar combination of tickets. You just need a reservation, which you can book at a station or via oebb.at (use the “Interrail / Eurail" discount).