Customize.el is not only about saving on keystrokes from elisp code, but it is highly discoverable, and importantly, type safe. If you need to put some wacky cons shenanigans to define your font locking rules or whatever, all that is taken care of you in customize.

I don't put the output customize.el under version control since I vary my settings somewhat from machine to machine, and I use version control to sync my emacs configuration. However the output is easy to mechanically transform into (setq-default) for things that I do want to synchronize.