"Convenience of distribution" is, by nature, targeted at application distributors which are not the end-users I (or the OP) claimed to be affected by the messaging.
So yes, I think the messaging in GNOME Software should be improved (hard for me to check on Ubuntu because it does not come with Flatpak support on by default).
Note that ".bashrc and similar" is a huge amount of files (just off the top of my head, .profile, .zshrc, .cshrc, .Xsession, .xinitrc, .ssh/config [for eg. ProxyCommand]... you get the gist).
So yes, I think the messaging in GNOME Software should be improved (hard for me to check on Ubuntu because it does not come with Flatpak support on by default).
Note that ".bashrc and similar" is a huge amount of files (just off the top of my head, .profile, .zshrc, .cshrc, .Xsession, .xinitrc, .ssh/config [for eg. ProxyCommand]... you get the gist).