There are GUI conventions which at this point have been with us for three decades, and no matter what operating system you're using the vast majority of programs you use follow them. I would never argue that it's impossible for a program to be improved by deliberately flouting those conventions -- but I'd argue that you need a defensible rationale for doing so. A sound system for a large space has different tradeoffs and design considerations than a home theatre system does, but it's actually following a different set of well-considered conventions, right? I don't think calibre's UX design is well-considered at all; I think it was put together by someone who doesn't know much about UX design, isn't willing to learn, and whose reaction to even gentle criticism is to dig in his heels.
I buy this argument for professional GIS software, database management software, etc. But come one, Calibre basically has 3 purposes: keep a library of ebooks, convert them between formats, transfer to devices. It shouldn't be so complicated. Every time I go open it I have to relearn how it works.
Then you must be doing something wrong. I use Calibre very infrequently, and yet I've never had any trouble remembering how to convert a book and load it onto my Kindle.
I'd like to see a few more jet-powered unicycles rides. They sound fun. Functionality, especially in niche software, is sometimes more important than some kind of idealised smooth workflow.
The nearest physical analogue I can conjure up is to contrast a 'sound system' as used in dances in church halls and community centres round here (wardrobe sized speaker cabinets with 18" paper cone speakers, horn tweeters, all patched into a rack based preamplifier that only the constructor and a few close associates know how to navigate) and a domestic hifi by (say) Denon. Both have their place.