Some sites are not loading with Unbound upstream

I think you need see if systemd-resolved is installed. I installed a clean lite version of 64-bit Pi OS Bookworm and it wasn't installed by default. You should have a /etc/systemd/resolved.conf file.

try:
sudo resolvectl

Note that I'm not using pihole on this particular Pi. Just Unbound. I edit the /etc/systemd/resolved.conf file and do a reboot and the /etc/resolv.conf file is generated. No setting of system links or anything. I think if I don't edit the /etc/systemd/resolved.conf file it will just use the system defaults and list them in the /etc/resolv.conf file after reboot.