In the Github thread, reduz commented on Sep 15, 2016:
callbacks get called at all levels, back when we had Squirrel
programmers used to forget calling the parent functions all the time
for callbacks they handled different and it was kind of a mess.
I've worked with an in-house game engine written in C++, and for some functions, forgetting to call the base implementation resulted in very bad behavior. Maybe the Godot engine devs made this design choice simply to avoid such situations?