2. It makes perfect sense if you actually learn how Emacs works. It provides superficial elements like GTK-look-and-feel (scrollbars, menubars). Most Emacs experts disable all of these anyway, thus nothing of value is lost. On the other hand, toolkit-less Emacs tends to be a lot more stable. That was definitely the case for GTK since it had well-known bugs that the GTK developers refused to fix that would crash Emacs. I suggest you compile graphical Emacs on Linux without any toolkit (or with Athena/Lucid/Motif) to see for yourself.

3. Because there are trade-offs involved and the (informed) user should be responsible for enabling them.