GNU is very strict on the definition of "free software" and anything that deviates from their (and by "their", I mean Stallman's) idea of free software is automatically marked as "do not endorse", which is usually very poorly worded and makes it seem like anything that is non-free software is the devil's work.
As far as I'm concerned, GrapheneOS does not advertise itself as being open source or free software, because that's not really the ethos of the operating system itself. Even if there is non-free software in GrapheneOS (which technically the Google Play Services installers could count as such, since they are built into the operating system), the main focus of GrapheneOS is security and privacy, not necessarily being free software and abiding by GNU/FSF's criteria for what free software is.
I mean, they don't endorse LineageOS because developers and maintainers add the proprietary blobs to each device they are porting the OS to, which is something that is MANDATORY for the system to even boot or function properly. They also claim they can't endorse LineageOS for having instructions on how to install Google Apps on the device. We're not talking about something baked into the OS like Graphene, but a written guide on the LineageOS website that no one actually needs to follow if they don't want to.