I'm not so sure that this is right. I have the extended battery and for the first time today drained it all the way down and the battery life "percentage" indicator turned out to be pretty much exactly correct. I think the phone somehow senses which battery is in there and adjusts accordingly.
By the way, battery life was 11 hours and this included two solid hours of screen-on continual LTE stock market quote streaming and all-day LTE email flow (albeit with only a few minutes of phone use). This is actually longer usage than I used to get from my 3G Blackberry Tour (using a standard size battery), as the the screen-on stock quote streaming used to be a real BB battery-killer.