Upon trial and error in a docker, I realised what follows.
xfce4-mime-settings reads associations in preference order from:
$HOME/.config/mimeapps.list
/usr/share/applications/mimeinfo.cache
Actual directories are affected by $XDG_CONFIG_HOME, $XDG_CONFIG_DIRS, and $XDG_DATA_DIRS and it is possible to have also a DE specific version of mimeapps.list with higher preference, such as xfce-mimeapps.list.
See Association between MIME types and applications
If the user modifies settings in xfce4-mime-settings, they are saved to $HOME/.config/mimeapps.list.
The file /usr/share/applications/mimeinfo.cache can be created from scratch or updated with the standard utility from freedesktop.org desktop-file-utils
sudo update-desktop-database
i still don't know if there is tool to bulk-populate $HOME/.config/mimeapps.list
With respect to my question, apparent idiosyncaracies are solved by inspecting the cache (mimeinfo.cache).