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Also, powered USB is 5V even. So even if the PRS charger is set at 5.2V, battery management should handle 5V just fine if it also supports charging over a USB connection.
The difference in charging speed is the amperage. Voltage is the chunk of electricity you get, and amperage is how quickly you get those chunks. The PSP charger and the PRS charger both supply 2000 mA, hence the speed.
USB provides a variable amount from 100 - 1000 mA as requested. Negotiation tells the USB controller how much to send to the peripheral, and the software in the device can adjust its charging style based on how much juice it's getting from the controller.
If I had to take a wild guess, I'd say the without the negotiation, the Reader plays defensive and blocks charging so the USB circuitry doesn't accidentally get wrecked (i.e., we don't know what amperage it wants -- it might only be rated up to 500 mA) at worst, and at best so that the rate of charging matches what battery management expects.
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