Advanced protection is a Google account feature and works fine with GrapheneOS...
The only difference is that on GrapheneOS, Google Play won't stop you installing apps from third party sources since it's a sandboxed app and can't do that via the privileged API it tries to use.
Also in regards to Play Protect:
Google Play Protect checks your apps and devices for harmful behavior.
It runs a safety check on apps from the Google Play Store [Before you download them].
It checks your device for potentially harmful apps from other sources. These harmful apps are sometimes called malware. [It can do this as like any normal app it can see what other apps are installed in the same user, this is not a privileged level feature and will be simply checking a package name against a list of their known malware. This won't work if it doesn't have network permission.]
It warns you about potentially harmful apps.
The following it cannot do as it doesn't have access to system level privileges:
- It may deactivate or remove harmful apps from your device.
- It may reset app permissions to protect your privacy on certain Android versions.
It CANNOT read your files unless you grant it the broad File access via the Photos and Videos or Music and Audio permissions instead of using Storage Scopes.