there are many apps which use root access to increase privacy

If you mean apps that allow you to restrict permissions of other Apps, there's App Ops, it works with Shizuku

customize the system

You can do some customization with adb/Shizuku but for some things you might need root. But I would definitely value security over customizability.

manage battery charging

The OS can do that pretty well

enforce firewall for apps and system

GrapheneOS has a built-in firewall that you can use to block network access to any app on the system.

block trackers

You can do that with DNS services like NextDNS

backup the system

GrapheneOS has a built-in backup solution