Thanks for the question! When you are setting up your add-on domain, you will find that you can change the path of your files there. You can change the path to not include the public_html folder, if that is your need. The main issue is that it just needs to remain under your account user name. For example:
If you need more information about the document root, check out our article Directory to upload files.
I hope that helps to answer your question! Please let us know if you have any further questions!
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