I don't disagree with your position -- I disagree with the implicit contention that calibre's non-standard UI improves its functionality. It is, at its heart, a file management and viewing application. What advantage does it get by spurning the notion of File and View menus? How is it made better by having a toolbar full of non-standard icons that literally duplicate the menu bar? Is it merely UX idealism that would lead one to argue that menus that have items twenty words long is needlessly suboptimal?

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.