They're not independent, they are indeed the system's. And while we freeze *some* parts of it, that probably won't help much.
It will *probably* download stuff in the background. It *might* not force-launch the update automatically (emphasis on *might*), *unless* you're on an SO device, in which case it very well might as soon as you suspend the device.
TL;DR: Using KOReader doesn't exempt you of taking care of blocking OTAs
.