Autoloaded variable overrides the one from the init file

I added the following line to my init file to replace ruby-mode with enh-ruby-mode:

(setq auto-mode-alist
      (mapcar
       (lambda (x)
         (if (eq (cdr x) 'ruby-mode)
             (cons (car x) 'enh-ruby-mode)
           x)) auto-mode-alist))

But it works only for the first file. The first ruby file I open is in enh-ruby-mode. But in the process the following command is executed:

/usr/share/emacs/26.3/lisp/progmodes/ruby-mode.el.gz:

;;;###autoload
(add-to-list 'auto-mode-alist
             (cons (purecopy (concat "\(?:\.\(?:"
                                     "rbw?\|ru\|rake\|thor"
                                     "\|jbuilder\|rabl\|gemspec\|podspec"
                                     "\)"
                                     "\|/"
                                     "\(?:Gem\|Rake\|Cap\|Thor"
                                     "\|Puppet\|Berks"
                                     "\|Vagrant\|Guard\|Pod\)file"
                                     "\)\'"))
                   'ruby-mode))

(The same line is in /usr/share/emacs/26.3/lisp/loaddefs.el.) Which means the second and the following files are opened in ruby-mode.

I guess to remedy this I’ve got to not change the line in auto-mode-alist, but add one. Anyways, how does this autoload thing work? When does loaddefs.el get executed? Is there a way to keep the line out of the file?