There's the installer,
https://github.com/kovidgoyal/calibr...libre/linux.py
The only call to chmod is on line 738, which is for the calibre un-installer and is used to mark it executable. There is nowhere in the installer that permissions on files in /usr/share/mime are changed. If the permissions on those files in your system are being changed, it is by something other than the installer.
As I said before, the installer does not itself install any mime type files. It calls the xdg-mime system utility to do that. So if mime files are having their permissions changed, it is because xdg-mime (or something it in turn depends on) is doing it.