I think your question is answered by the thread you linked. Is there something in particular you don't understand?

GNU/the FSF says that GrapheneOS does not qualify as free software (which is true, it's not completely FLOSS as per the FSF's definition—the linked GNU article classifies plenty of popular Linux distros we consider to be FOSS as non-free, btw, they're not singling out Graphene), and GrapheneOS is saying they don't want to fit the FSF's definition of free software because it would mean a lack of security (which is also true; they need proprietary firmware updates from Google). The FSF has a strict definition of free software which a lot of software does not meet, and usually an entire operating system would only meet the FSF's definition out of a deliberate, conscious, ideological decision to exclude all non-free software. In their article they even list Debian as a distro which no longer meets their standards, despite Debian being known for their strict policy around only including FOSS in their repos.

This is an instance of two different entities (GNU and GrapheneOS) having fundamentally different goals (one values a strict definition of free software at all costs, one values security at all costs). You are more than welcome to do things GNU's way if you don't like GrapheneOS's way, or vice versa.