cpanel addon domains - better way?

usualy, cpanel automatically add addon domains to /public_html folder. say i want to add as addon domain, cpanel will put it into /home/username/public_html/

this way might give few problems.

first, if search engine find it, it will hurt your SEO. because you have duplicated content and your domain could be marked as spam. so, if you do this, dont let search engine knows it.

second, management problem. if you add few dozens domain, now you public_html folder will be messed up with dozens of folders not related to your main domain. very inconvenient.

maybe you can point out more problem you encounter with this?

for me...
i simply remove the public_html and put the addon domains directly at my home folder. so if i add i will put it at /home/username/

this solved all my problems.
what do you think...
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