This is not qubes specific but just in general.
It seems to me there is some confusion here and the “in general” looks like the key.
While the rc.local (in the context of traditional init in *nix) is legacy, there is no document which says that /rw/config/rc.local is deprecated, legacy or discouraged to use in Qubes OS. On the contrary - it is an essential mechanism for customizing an AppVM without touching the template. In a previous discussion, it has been clarified that it is not possible to create and enable an AppVM-specific systemd unit without modifying the template too.
So, perhaps the confusion comes from the identical filenames.