( I always prefer to see the extensions too though :) )
That’s not exactly an answer to your question, but there’s a chance it’s an acceptable solution, so duly noted.
Or just use the file suffix, which is AFAIK what all the mainstream Linux desktop environments do, through Freedesktop's MIME implementation. I don't know if it supports using metadata or file magics instead, but a quick glance shows almost every MIME definition uses file globbing.
You can check this in the files located at "/usr/share/mime/application" and "/usr/share/mime/packages" on most distros. Most (all?) definitions use a "glob pattern" to match files.
Finder does try to help with renaming and when you try to rename a file only the filename is selected and not the extension.
In GNOME for example gio handles opening files in the "correct" application by way of the MIME database in /usr/share/application/mimeapps.list and ~/.local/share/applications/mimeapps.list.