this is  general  in Mate. Same on debian (stretch) matedesktop.

xdg-mime query default application/x-desktop
userapp-pluma-JPST30.desktop

this desktop file appears under $HOME/.local/share/applications/

cat .local/share/applications/userapp-pluma-JPST30.desktop 
[Desktop Entry]
Encoding=UTF-8
Version=1.0
Type=Application
NoDisplay=true
Exec=pluma %f
Name=pluma
Comment=Benutzerdefinition für pluma
alex@Taomon:~$ 


even with xdg-mime itself I can not change it to pluma.desktop

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https://bugs.launchpad.net/bugs/1929307

Title:
  It is hard to set Pluma as default application to open desktop-files

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