The point is that no one is doing arb trading otherwise the spread wouldn't exist! (or it is probably some whales with priority wires taking advantage of the spread). So in the context of tracking the price variance, one would choose daily values since this variance has existed for over 2 months.
You can do arbitrage trading between exchanges without actually moving any funds. It won't be possible to take advantage of the current crazy MtGox situation, but as long there are only fluctuations around a fairly fixed spread you can buy on one exchange and sell on the other when the difference is one way, and trade the opposite way when the difference switches.