having multiple domains under one hosting

When you have multiple websites under 1 hosting plan, obviously one of them needs to be the mail domain for that hosting plan, and the other domains appear as separate folders under that main domain in your ftp panel but regardless of that they are still totally separate websites. does the main domain get an advantage over other names because of this? or do the other domains listed as separate folders get a disadvantage? – in terms of SEO, or any other thing?