Does it really matter if [project].github.io is used when github.com/username/[project] will exist just as long if not longer? Also, I've been noticing a handf

Does it really matter if [project].github.io is used when github.com/username/[project] will exist just as long if not longer? Also, I've been noticing a handful of project sites hosted at github.io that apparently once used to work have been returning a "site has been disabled due to a misconfigured custom domain" message. I realize its a configuration issue but this is just as annoying as a custom domain like rivetsjs.com potentially disappearing.