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Why can't it infect (the microcontroller on) the battery, and then infect your device later?

There are dumb batteries that only use the power connections. Those can't be infected.

Ostensibly you're using that aforementioned power-only cable from battery -> device.

But then you can just skip the battery anyways...

If the untrusted charger has a USB socket, then yes. If you have an untrusted charger with non-detachable cable, then no.