I feel the title of the thread is very descriptive. I don't find a way to force caja to show all files extensions. If Caja knows the file type, it will automatically hide it's extension.
Using Caja 1.22.2 (recently updated by update-manager) on Ubuntu MATE 19.04.
Ubuntu doesn't need to have extension to a file to know its type. Caja don't hide extension file. Most of file created in Ubunty don't have extension, no need. Just add extention to file to see that caja don't hide it.
I agree with you, but you know that that doesn't solve the issue.
Look at this
Hi @chexmo, You found the only exception I know of. That is, *.desktop files.
For quite a while Linux file managers have been displaying some internal title (I'm not sure exactly what) and I thought it was from this spec but I'm unable to locate exact details I thought I tracked down years ago. I can assure you it's not just Caja but every file manager I've seen.
I invite a developer to jump in and add some reasons. It never thrilled me, either. 
Same issue on Lubuntu 20.04 for .desktop files:
Same on Xubuntu 18.04:
