I am not asking anyone to change suit my needs. I overcame the problem by simply using a fake domain (stupidfakedomain.com) that I do not own for the default user domain. Then the public_html will never have any files.
There is no logical reason why creating an addon domain also creates an addon directory, but default domain does not get its own directory under the public_html directory. Like you said, they all do it. Its not a big problem, but its just chaotic when i explore my main domain and see all these other addon folders sorted alphabetically amongst my default domain files and folders.