I am wondering the same thing. The way I understand it, is that these are just fork of the AOSP apps which maybe don't have the Material You theming. It isn't really surprising. Google has been taking more and more of their apps into a closed source environment.
I personally use theirs. They look better and are really well made. I just tend to you disable the network access on most of them. I use Gboard, Photos, Contacts and the Recorder, network disabled. I use their dialer also, with network on for the spam filter (spam calls are a big issue in my life).
Graphene will have to make their own or find better suitors in the open source world. I think they already said that they wanted to eventually revamp or maybe completely changed those default apps.
As for now, if you want some good default apps that follow Material You theming, check out the Simple Mobile Tools suite of apps. They're fully open source and you'll find them on both the Play Store, and on F-Droid. :)