As you know, GrapheneOS is based on AOSP. GrapheneOS includes apps that are included as part of AOSP. These AOSP apps aren’t maintained by the AOSP project as well as, really, anyone would like.
For clarity:
Included AOSP apps are: Calculator, Clock, Contacts, Files, Gallery, Messaging, Phone, and Settings.
Included GrapheneOS developed/maintained apps are: Apps (for updating GrapheneOS maintainted apps), Auditor, Camera, PDF Viewer, and Vanadium
The GrapheneOS project covers the project’s approach to apps here: https://grapheneos.org/faq#bundled-apps
My approach to included apps I don’t wish to use is to disable them. Disabled apps aren’t displayed in the app drawer, etc. and can be re-enabled in ‘Settings’. (This may not be true for the AOSP apps?)
Users can use any app from either Google Play Store or alternative “app stores”.
Messaging alternatives that are sometimes mentioned here are: Google Messages (often for RCS support), Simple Mobile Tools’ “Simple SMS Messenger”, or QKSMS (last release was Feb 2021)
I’m not sure it’s correct to assume Lineage apps are higher quality than the vanilla AOSP Messaging app – LineageOS Messaging is also based on AOSP’s.
This part is from memory- iirc nearly a decade ago when GrapheneOS project was getting started (It was Copperhead then) CyanogenMod, the progenitor of LineageOS, was considered for the base, but quickly rejected as a poor choice for a security focused OS. At that time CyanogenMod was notoriously lax e.g. about consciously leaving SELinux in permissive mode… I don’t know the state or security posture of that project now.
I hope some of this was useful or informative. Happy computing :)