It's a change in emacs-27, from etc/NEWS:
** 'print-quoted' now defaults to t, so if you want to see
'(quote x)' instead of 'x you will have to bind it to nil where applicable.
So binding print-quoted to your desired value and then saving a
customization should be enough.
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 region. custom-set-variables only contains assignments written by the packages I use.
If your custom-set-variables region is still in your init file, you may want to move it ...