I ended up factory-resetting the phone. Deleting the secondary user continued to cause problems with apps, weird stuff like Bitwarden not being able to connect to the server, etc. It took me about 4 hours to re-install 93 apps, some of which still needs configuring. I am now using the Owner account and can receive SMS messages; however, messaging app still does not respect the customized notification sound settings and keeps playing the default one. I am not sure yet if the customized ringtones are respected.
Coming from Pixel 5a, these changes feel like regression to me, since everything was working as expected there. I am also not a big fan of optic fingerprint reader, but the rest will hopefully go smoothly.
I still prefer GrapheneOS to any other alternative, as much frustrated as I may sound. It's got the right values at the right places, and the rest is more tolerable. I cannot imagine how much work and self-sacrifice it took to get it to where it is now. Huge thanks to all developers and maintainers!