I agree with you regarding the courtesy of DB station staff. In 2008 at Erfurt after a bus bridge through Suhr made me miss a connection they hand-wrote on the margin of my home-printed ticket an ICE connection via a Leipzig cross-platform transfer as a substitute for my 2nd class trip through Halle. I can now say I've visited Leipzig, though being on the platform for four minutes might not count.I think if you have a CIV ticket the connection will be honored , no matter the routing . You might have to buy that ticket from a travel agent or station though as I don’t think any online system will give it to you .
you can in fact book via any reasonable route and the same applies .
if you book the journey as two separate legs on totally different tickets then indeed if the train is late you are on your own .
that said, my experience with DB station staff in Germany is that they do go out of their way to help you , even if they don’t need to or have to . I once missed a night train entirely through my own stupidity and the kind lady in the ticket office worked out a way to get me onto a later train at only minimal extra cost .
The Bistro attendant on the last leg into Berlin was also good-humored and wasn't packing up early.
Before the bus bridge the conductor was informing us of it with her Saxon accent. There was a Chinese passenger who did not speak German and the sehr ernst conductor struggled. The Chinese visitor's English was good and I had read about the reconstruction work on the former GDR line, so we teamed up on the bus bridge to Erfurt, where his uncle was waiting. The conductor indicated relief.