FWIW (different model), My PRS-950's manual doesn't even mention that charging happens via computer USB connection even though it does. Their standard recommended charging procedure is to use the plug-in charger, which, btw, goes into the USB port (no barrel charger on this model).
I would think that a properly filtered mains charger would always be a better choice. Likewise, I would never leave something like a reader plugged into a USB port on a PC that was going to be power cycled - power transients when turning on and off can do very bad things to sensitive low-power electronics like the reader.
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