Comment # 1 on bug 1142275 from Malte Kraus

I believe this is already handled the way you wish:

  # touch /tmp/test{1,2}
  # echo "/tmp/test1 root:bar 0600" >> /etc/permissions.local
  # echo "/tmp/test2 root:root 0666" >> /etc/permissions.local
  # chkstat --system --set
  Checking permissions and ownerships - using the permissions files             
          /etc/permissions                                                      
          /etc/permissions.secure                                               
          /etc/permissions.d/postfix                                            
          /etc/permissions.local
  /tmp/test1: unknown group bar
  setting /tmp/test2 to root:root 0666. (wrong permissions 0644)

Maybe the error message should be more clear about the fact that execution
continues.