Why does buying an affordable train ticket always involve a treasure hunt of weird ticketing combinations and cards like this?
In the end the cheapest option was not to use a BahnCard 25 or 50 but to buy two one-way tickets for each leg from the regional transportation provider via a smartphone app, because smartphone tickets are sold at a discount. It's wasn't just a bit cheaper but about 30%.
One thing I despise about trains in Germany and France is that the experience still feels way too old school. What happens when something is delayed or when a connection has an issue makes you feel back in the eighties. The Deutsche Bahn applications are a great way to see that, it's confused and overly complicated. I wish the UX of apps/websites like https://www.trainline.eu/ would be the standard by now.
My tips would be:
* Book at least a week in advance.
* Buy a Bahn Card 25.
* Get up early.
If you do this Berlin -> Munich is €44.90 next Saturday on the 4 hour fast train. Also don't forget, it costs around €11 to go from Munich airport to the city.