FYI. If put (package-initialize) before custom-set-variables,

>>> before custom-set-variables : 3.637 sec <<<
Loading image-file...done
Loading time...done
Loading completion...done
Loading elec-pair...done
Loading icomplete...done
Loading ido...done
Loading avoid...done
Loading savehist...done
Loading paren...done
>>> custom-set-variables time: 10.080 sec <<<

Don't know whether autoloads being triggered. It is hard to test one by one.

On Mon, Mar 12, 2018 at 9:52 AM, Noam Postavsky <npostavs@gmail.com> wrote:

Shuguang Sun <shuguang@gmail.com> writes:

> Thank you for your patient explaination. I put the (setq
> package-enable-at-startup nil) in the early-init.el and the load time
> of .emacs is the same to the emacs Feb version.

Oh, interesting. I guess the slowdown of the custom-set-variables must
have been caused by autoloads getting triggered then?