If it helps to think of Calibre as a "toolkit," then, instead of a single monolithic app, I'm all for it.
It's funny, if they released a version of Calibre that had only the bins you mentioned and omitted the GUI entirely, it would probably be held in much higher esteem among the HN community.
I’d argue this is true in general: I once gave a presentation about a (IMO) pretty decent tool but made the mistake of demonstrating it with a UI that was usable but needed work. It got a lot worse of a reaction than an earlier and worse version of the same tool where I ran it from the command line.
It's funny, if they released a version of Calibre that had only the bins you mentioned and omitted the GUI entirely, it would probably be held in much higher esteem among the HN community.