The PMIC (power management IC) has RTC capabilities, including wake-up. So yes, it can wake up from "almost off" mode (i.e. only PMIC powered).
Of course, the Kindle can wake up from it's normal "sleep" state at any time by normal software control. It's still running, after all, though it has nothing to do and the SoC has a quite good low-power idle mode.
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