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No doubt the AMF and the ship's ancillary systems could be tuned not interfere with each other, or not as much. Or some kind of AAMF physical shielding.
On the subject of WAS drones, I would see it thus- their virtual materiality- with no real physical component (aside from gas molecules perhaps, used to stabilize the magical drone construct. I would further imagine that the drones don't have or need any kind of line of sight or controlling link, perhaps being interfaced with Nanoha and Raising Heart on the same level as something like mage-telepathy
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