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> Is there any way to be certain these are done in hardware and can’t be caught in a low level system once the device is rooted?

If you suspect your device has been tampered with and need a guaranteed reboot, just let the battery run down and don't use it until it has.

> If you suspect your device has been tampered with and need a guaranteed reboot, just let the battery run down and don't use it until it has.

Just a (overly paranoid) thought: a sophisticated attacker could simulate a drained battery and subsequent reboot, no?

No sophisticated attacker can make a phone run for five days without recharging. Just leave it on for five days and you should be fine.