It makes a difference in that if you buy it from Border's you're reinforcing their decision not to allow returns. If you buy from Sony, you're reinforcing their much more liberal return policy.
The free book offer is from the Sony Connect store and comes with every reader, as I understand things, when you register it (authorize it) at the Sony Connect store, so in that regard it makes no difference where you buy it.
As for the extended warranty, that's a gamble you need to decide on whether it's worth it. In general it's a huge profit center for whomever you buy such a plan from or they wouldn't be offering it for sale. That means they are convinced that for every X policies they'll sell they'll only need to make good on 1 or 2 of them and the rest of the income is pure profit over and above what expense was incurred in satisfying those few claims.
As I once read life insurance explained in the comic strip "Wizard of Id"
Salesman: We're betting that you will live longer than the length of this policy.
Wizard: What happens if I die before the end of the policy?
Salesman: You win!
The only time I've ever bought an extended warranty policy, the part which broke on the car it was guaranteeing was listed as a "wear item" and not covered. My wife, on the other hand, has gotten 3 replacement handheld cassette recorders from Radio Shack under a $30 policy she bought.
Finding out how many members of this forum have bought extended warranties and actually gotten a repair/replace reader under such a policy might be a good thing for a poll.