With powertop you see also processes that wake up cpu in idle state. It's not all about cpu percentage but how often cpu is awaken also one of biggest battery drainers for me was wlan driver in first firmwares, but it has been since fixed.

And IMO your idle state cpu usage is huge in comparison to mine (almost none, read wiki and threads about "normal" cpu usage when you are running on bare minimum load/settings/apps). On the other hand I do not use any online activity apps when idle.

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The best way to start looking for answers is IMO always to turn off everything and start starting stuff gradually and see how it effects to whole system. And if bare minimum state is still draining then it might be time to flash emmc+rootfs and not restore same apps that were before.

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IIRC Powertop shows also some IRQ activity stats.