Is Addon domain affecting SEO

Question

addon.com
main.com/addon
addon.main.com 

these are the 3 ways i can access the addon.com are the urls indexes distinctly is there anything to prevent  this  and does the search engine consider consider addon.com as a subpage in the main page

Answer 1

search engines wont automatically link your addon-domain or subdomain to the main domain

 if  there is no index page to a public html & if your subfolders are exposed then there is a chance  of the search engine linking them

robots.txt may help you so please try it out