Hi, on one day you can add the journey from Venezia Mestre to the station before it crosses the border. For the day after you can add the journey from the station before the border until your final destination, which will be counted as your inbound travel day. (if these journeys cannot be found in the app, you can add it manually - at the bottom of the planner, there is a blue hyperlink '’add it manually'’) 

Have a look here (the blue hyperlink under '’travel days'’ section), for the step-by-step explanation on how you'll have to add the journeys when travelling home by night train. 

Thank you for the help! 
Luckily I have an extra travel day left over, so I can do it this way.

Would there otherwise be the possibility to count an over night train toward the following day? 

No as for Nighttrains counts the day of depature rule means for your onward joruney from Munich you still need a travelday the only problem here is that the system doesn´t notice when you cross the border and because of that select as inboundday the day of depature of the Nighttrain :)

the workarround with selecting Salzburg is just to get the Inboundday on the correct date :D