I am looking into this. Here’s a .desktop file from one of these PWAs installed through Brave:
Exec=/nix/store/qw0yx6qgnkg5r8az93lhmcqpaagjskiy-brave-1.60.118/opt/brave.com/brave/brave-browser --profile-directory=Default --app-id=pjibgclleladliembfgfagdaldikeohf
So you’re saying that instead of /nix/store/... the Exec= line should use a relative path?