Yeah, but that’s about it. Fairphone OS has and will have a custom launcher, but you can install any launcher you want to anyway. Even ones that give you the look and feel of iOS.
Other than that the Fairphone also comes with a few custom apps.
Of course I have not held a Fairphone 2 in my hands yet so I’m not 100% certain that the Fairphone 2 won’t have any other substantial differences to standard android, but the infos we got so far didn’t indicate anything of that kind.