While I haven't looked at the B&N warranty, MANY manufacturer's do indeed consider rooting, etc. to void the warranty, which I find to be ridiculous as it harms the device in no way, or no more so than their own updates.
I'd guess that the manufacturer concern wrt rooting would be non-technical users rooting, messing something up and then calling tech support for help, but beyond this I can't see any problems that would not otherwise possibly arise on an unrooted device as well.
Now if you can restore stock fw and have the same level of functionality with whatever problem, I see ABSOLUTELY no reason NOT to exercise the warranty, as the problem is obviously still present in the stock condition.
Reverting to stock and not everything undone: They are likely referring to the fact that the data partition is not wiped, yet you could take the time to manually wipe them or likely someone could provide an update variant that does this as part of the process. In any event if you can get to a factory reset option that SHOULD wipe everything down to just like it came OOB, if it's a properly function factory reset.
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