The FOSS author has a choice: they can attempt to chase whatever UX rabbits are scared up by The Market, or they can try to make it straightforward to learn their tool, despite its differences from the momentary fashion. I think the Calibre dev's done an excellent job there.
Maybe there is a reason people do spend years studying interaction design, and we can agree there's probably things that could be improved on the interface to make it more intuitive by someone who's specialised in that?
> articulating "what I'm used to".
This is true, but most users spend most of their time away from any given application. Very few people become experts at using Calibre. So there's nothing wrong with taking cues from the most popular applications, the kinds of applications where people form their intuitions.
I use Calibre a few times a year, and I'm quite confused every time. I usually just Google the steps to do the thing I need to do, and even after I understand how to do it, it never makes a lot of sense to me.
Having said that, if the developers like the way it works, then that's all that matters. I'm glad it exists either way.