Calibre (Ubuntu) sets itself as standard-app for a lot of file types not related to it

Lots of those aren't actual filetypes and are probably being included
because they are just text/plain, which is a valid ebook format.

None of this actually matters, though. It's not really calibre's fault that
it allows itself to be a right-click option to open with.

For all of Linux's many excellent advantages, and even despite Linux's
vastly superior desktop database for handling *allowed* mimetype
associations, the actual defaults system is frankly abominable. Any
mimetype that doesn't have an explicit default set is considered
"unspecified default" and the specification says that your Desktop
Environment is allowed to choose which program to open your file in by
picking it out of a hat.

In practice what happens is that they use the first one listed in the
system cache. This cache is randomly generated and simply installing a
program which doesn't even handle text files, will regenerate the entire
cache from scratch, and shuffle the order, thus changing which program
actually opens text files.

So every time you check, you might see a ***different*** default
application. There's no way to win against this, other than by manually
using "set as default". The problem is not limited to calibre.

For great joy, try installing a program such as Anjuta which declares
itself capable of opening inode/directory, at which point your system may
arbitrarily decide to cause things like plugging in a hard drive or USB
flash drive to launch that program instead of your file browser.

 status invalid

calibre does not advertise handling for any ofthose file formats. I
suggest you uninstall the distro based calibre and install the official
binary from https://calibre-ebook.com/download_linux

I have no idea what the ditro package does. The official binary
advertises support for only the following, which are all very much ebook
formats:
text/html;application/x-mobipocket-ebook;text/rtf;application/ereader;application/x-mobipocket-subscription;application/oebps-package+xml;text/x-markdown;text/plain;application/epub+zip;application/pdf;application/vnd.oasis.opendocument.text;application/x-cbr;image/vnd.djvu;application/vnd.ms-word.document.macroenabled.12;application/x-cbc;application/xhtml+xml;application/x-cb7;application/x-cbz;application/x-mobi8-ebook;application/vnd.openxmlformats-officedocument.wordprocessingml.document;application/x-sony-bbeb;text/fb2+xml;x-scheme-handler/calibre;

 status invalid