EWS It sounds as if the system's integrity protection worked as it was designed to. I suspect if you built your own derived OS with appropriate package manifests etc. then it would pass its own integrity checks.
If you do go that route, it would be important to re-badge your OS and not to refer to it as GrapheneOS. And also to configure your OS to not hassle the GrapheneOS update servers.
Please note that I don't speak for the GrapheneOS project.