[Adoby]

There really is no point in having packages installed that are not needed. Just unnecessary bloat.

Why would you want to keep unused packages? If they ever are needed again, by some other package, apt will install them again.

The binary install for Calibre includes private versions of all the dependencies. So there is no need to keep, maintain or install anything else but the binary install. When you update that, all the private dependencies are updated as well. It may be a little wasteful of hard disk space, but it sure saves a lot of time not having to install and update and maintain a large set of dependencies. Kovid has all that sorted and tested for you in each new release.

And Calibre doesn't spread a lot of files everywhere. Just remove one folder and you almost all of Calibre is gone. Not anything that can cause any problems.