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You can run Shizuku in ADB privileged mode (running a shell command through ADB that starts a service so other apps can access that same privilege), or run Sui, a Magisk module that provides a same service but with root access instead. The ADB privileged version doesn't trip Knox since it doesn't require unlocking your bootloader, but Sui/Magisk most definitely will.
Exactly, in other words, Shizuku is safe if you are afraid to lose the guarantee of your device, Shizuku are simple ADB commands (not so simple) and ADB is a tool known and used by developers, there is nothing wrong, it would be like losing the guarantee of a Windows PC by using a script to delete Edge (And so, there are GUIs that use background commands)
Now that I think about it, I'm not sure that Automate currently natively supports running commands with the Shizuku service. It uses its own privileged service that does practically the same thing. If you're really desperate for using Shizuku, you could look into using the rish adb shell that Shizuku provides, but I'd suggest trying out the native privileged functionality in Automate first.