> From: Raoul Comninos <revcomninos@gmail.com>
> Date: Fri, 24 Apr 2020 12:49:02 +0200
> Cc: 40796@debbugs.gnu.org
>
> Yes, even if it is empty.

Then I cannot reproduce this.  I made a .emacs file with only the
following:

  (require 'org)
  (org-babel-tangle-file "~/.emacs.d/settings.org" "~/.emacs.d/settings.el")

and then started Emacs 28, changed the default font, and saved the
options via Options->Save Options.  Then I restarted Emacs, and Emacs
was using the font I changed.

Are you using the version of Org that comes with Emacs 28?  Or are you
using a different version of Org?