The main difference between using a boost circuit and a buck circuit (one that uses stacked batteries) is that generally, if you are using a switching power supply circuit for both the buck will give you longer battery life. A boost circuit, which usually is more compact and convenient (because there is only one battery) will have a lower battery life than a buck circuit.
As far as the size is concerned, well, that is a function of your ingenuity with the design. I think we've shown with the eGo Booster, you can make a boost circuit that is pretty small. The only reason its limited to 4.7V output is because that's all you can reasonably expect to get out of an eGo Battery, so the voltage limitation is a limitation of the eGo Battery, not the boost circuit.