Perhaps the A->C ticket entitles you to travel on either an air-conditioned nonstop high speed train, or a slower train that stops a lot along the way, and buying A->B and B->C tickets you can only travel on the slow train and that's cheaper.
Perhaps all the discount advanced-booking tickets leaving A have sold, mostly to people only doing A->B, and when you look up B->C there are discount advanced booking tickets still available.
Perhaps you depart A during peak hours and so pay a peak fare, but as the B->C portion of the journey starts later, it doesn't fall into peak travel hours.
I would say you need to compare DB to other Western European railway operator/networks. In my personal experience, DB comes dead last and it's not even close to the 2nd to last. Renfe (Spain), Trenitalia/Italo (Italy), SNCF (France) have much better services, at least on the long-distance routes (> 200KM). So much so that they are a viable alternative to domestic flights.
Additionally, most of those countries also have a much worse geography to contend with (e.g. Italy with the Alps and Appennini) and they still manage to have a nice high-speed rail network that works.
Finally, answering your last point, Japan still is THE role model. So much so that you can get stuff delivered to a train station your train is transiting through (at least with the Shinkansen lines) because the carrier knows exactly when your train will be there. I was astonished by that.
Berlin-Munich
In France, Paris to Lyon is 2 hours by train and there is simply no way going by car is faster (legally).
These are just examples, my point is that a high-speed line should be a lot faster than going by car. Not slightly faster, and sometimes even slower.
And those longer trips wouldn't even count as delays since they were hopefully announced weeks ahead of schedule and so passengers know it will take longer to get to their destination.
Having seen the US attempt and lived with the UK railway, the German one is definitely a huge improvement. Yes, it does go wrong sometimes, but my experience at university in the UK was the end of term had two carriages with twice as many passengers as seats, that regularly terminated 20 minutes before the official destination, and my experience visiting the UK now that I live in Berlin is that the UK rail fares are (or often were pre-pandemic) more expensive than the flights to the UK. There's even a standard "money saving trick" on UK fare prices where you split a journey from A to B into A->C, C->B, where C is one of the stops in the route from A to B so you don't need to disembark.
That doesn't mean there's no room for improvement, neither the UK nor the US railways are role models. (I assume Japan is still a role model for rail? Not heard much since the 90s…)