I forgot to continue writting:
In this later case of misbehaving .desktop file, it's often needed to
*copy* the .desktop file that is made available in the Guix profile of
the current user, and modify it for your needes. When done, perhaps you
can send a git/unified patch to Guix project so that they apply your
modifications (and you also get the chance to put your copyright holder
line in the relevant files, so you can participate in some decision
making and license compliance enforcement in the future, if you so desire).