This point-and-click seems like a useful feature for editing, *if* it's
configured to work on your system. But it apparently is not usually set
up that way by default, at least on most Linux systems. (I do
appreciate the instructions in the manual for configuring it, and plan
to do that.)
I think pretty much everyone uses point-and-click. The most popular editor (Frescobaldi) is available on Linux (I use it) - often packaged for you by the distro, so I think you are not correct about how it is typically used there. If you were in the dark about this until now I think you are an outlier. Working with LilyPond is much harder without it.
Re the greater point about whether it should be on by default: I personally like it as is and wouldn't want to have to enable it each time or make new users do it. And I think that is more important than the potential downside of someone not knowing to use publish (or forgetting), and then making a pdf available that reveals their system username. But that is only my opinion, and I understand your view.
Kevin