Had a similar problem when changing the default application for pdfs between e and plasma.
My impression is that the kcm module still writes to
.local/share/applications/mimeapps.list but now the correct path is .config/mimeapps.list
(or kde-mimeapps.list if you want DE specific) so your changes are ignored.
You can try to
mv .local/share/applications/mimeapps.list .config/kde-mimeapps.list