Ok, sorry to spam this thread, but I just want to leave the conclusion here in case anyone searches again in the future. I tested a bunch of stuff, including building a setup with capacitors in case it needs a surge of power mid boot (as it launches the framework). The answer is that you can wire directly to the pins on the kindle itself and then it doesn't see these drops (I wish I'd tried that properly before I wasted all this time testing).
You still need to disable the option in the power file to tell it to skip shutting down when it can't sense a battery, but then it does work. I am 3d modelling a "battery" that has the pins set up so you can pop it in place and put a little hole through the back so that It makes a nice hot-swappable plug, but then I am done
tlddr - connect to the power pins on the kindle, not the ones on the inside of the battery.
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