Ideally the system would be extremely smart: not just freely circulating anything, but tracking the health of each and every battery, doing automated maintenance as much as possible, and circulating certain batteries out for refurb if they get too low.
It should be like battery insurance: you'd just never have to worry about it, and there would be an extremely smart system ensuring the health of every Tesla battery on the road. "Should" being the key word here... but maybe that's the plan, hard to say.
Paying the difference between the two packs seems like it is that insurance, you just have to pay for it. Of course, we don't know what that difference is going to be so, so it's hard to say if it's a fair price at all...