In custom install profile How to delete the "Footer" menu that core provides by default?
Solved.

Following https://drupal.stackexchange.com/a/186322/8938  I added the code below to  my_profile_install() function inside my_profile.install file. 


  \Drupal::configFactory()->getEditable('system.menu.footer')->delete();


Reinstalled and yes, footer menu is not around anymore :)