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If behind the USB port is some (writeable) data storage (for PDF manuals etc) this is quite possible.

Or some infectable USB controller is involved.

What on here is able to store malware? https://learn.adafruit.com/minty-boost/parts-list

If the USB chargers in cockpits are any more complex than the above, why?

They almost certainly aren't USB chargers. Probably USB ports for inserting thumb drives to update the navigational charts. These kinds of USB ports are [mis]used for charging phones all the time, and the phone can end up being mounted as a mass-storage device.

No idea how the rest of the exploit would work in this scenario though, I have a hard time believing it.

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