I thought it would be aethetically pleasing to see well cleaned up init.el file
Yes, and in my case I don't use the customize UI at all, all my config is out of the
custom-set-variables only contains assignments written by the packages I use.
custom-set-variables region is still in your init file, you may want to move it to another file, copying from my config copied from Purcell's config:
(setq custom-file (expand-file-name "custom.el" user-emacs-directory))
(unless (file-exists-p custom-file)
(write-region "" nil custom-file))
(when (file-exists-p custom-file)
One thing to note is that
custom-set-variables can trigger the custom
set behavior written by the package author, while
setq cannot. Such behavior is defined in
:set when using
defcustom (read the doc of
defcustom for more). use-package's
:custom, obviously does trigger that, as its name states.