If I were to take an overnight train (eg: Aug 9 to Aug 10), the night rule says I will be charged for only 1 travel day if there are no train changes after midnight. However, most of the routes require at least 1 or 2 changes throughout the midst of the journey (some even requires 5 changes!). Does that mean everytime when a train changes take place after midnight, I will be charged for 2 travel days? Even if my travel day is only activated at like 23.55pm (means it will only last for 5 mins for that travel day itself)? In that case buy a normal ticket from your station to the first stop after midnight :)

Yeah it´s clear
If you board for example the Vienna 19.42 to Bucharest 16.40 next day Nighttrain you just use the depature day as travelday. Same applies for the 20.40 Milan to Siracusa/Palermo (arrival Afternoon next day) Nighttrain thats the best examples for the new Nighttrain rule.

On routes like Zagreb - Villach - Rome where you change aftermidnight in Villach the trains it cost 2 traveldays.

Which of your route have 5 changes? Just note the Railplanner is not really clever for example the Berlin to Budapest Nighttrain is showed with 3 changes (in Wroclaw,Bohumin,Breclav) but in real it´s a direct train with a own trainnumber (I add these journey´s then manual with the informations of the other railplanners like DB Navigator or bestway the local railplanner app)

 

I am asking based on the night rule below that I found on the Eurail website: 

When traveling on a night train that leaves on one day and arrives the next, without changing trains after midnight, you only have to spend 1 travel day: the day of departure. If you do change trains after midnight, you have to spend 2 travel days.