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.
Thanks for mentioning this. I didn't know that Calibre packages its own optipng, a program for which there have been some security advisories in recent years. I hope Calibre keeps pace with upstream releases of these tools.
I installed it on one server that I only ssh to JUST to use that ebook-convert so I can read anything (epub, mobi, pdf, etc) on the command line. It's so easy to use, detects to- and from-formats from filenames and works on anything.
Here's what's under calibre/bin
You can use many (possibly all) of these independently of the UI.