First, it would be nice if someone can see if they can reproduce this on GrapheneOS. I will later if I have time.
It's important to note that the "proof" for VPN "leaks" is setting up a dummy VPN on Wireguard. This could be a problem with their app, not with Android (and therefore not GrapheneOS).
It's also important to remember that computers are stupid and programmers sometimes fail to plan ahead for odd things to happen. In this case, misconfiguration can very well lead to unexpected behavior. So far, there is no evidence that Google apps can bypass the VPN on the stock OS or GrapheneOS when a VPN is properly configured.
Edit: I just tried on my phone with multiple dummy configs. I even copied a config from screenshots I found in the forum linked in the OP. I am NOT able to reproduce this. Notifications only come through when I connect to a correctly configured WireGuard server via the WireGuard app.