You should probably complain to the freedesktop people.
All calibre does is install *.desktop files for the GUI applications it offers.
`update-desktop-database` is responsible for reporting on available file associations, and also for randomly setting defaults.

This has nothing to do with calibre and everything to do with Linux standards for mimeinfo.
Somewhat related recent discussion:
https://www.mobileread.com/forums/sho....php?p=3299856