Ways URL structure can effect backlink efforts

Hubpages not too long ago had to change there domain structure from a subfolders to subdomains. So new pages would have the username. and then their main domain after it. My question is doesn't this affect the number of backlinks that any new page created within hubpages gets. If you were to do backlinking on the subdomain then it would carry over to the main domain since it is treated as a seperate URL right? Also, if you were to have a lot of backlinks for the main domain and other subfolders within hubpages then they would not pass on to any new article with the second URL right? Why did hubpages make the switch to the subdomain URL structure when it really effects their ability to give new pages the authority from the main URL?