just filter it in your app if you want it to say 100 percent... Assume battery low will be 0 or something, and rescale whatever perentage device says after it comes off charger from 0-9x to 0-100..

Other dirty little secrets: 0 percent isn't 0 either. Depending on use patterns you'll see it jump very fast from some low level to "battery empty", and/or then it'll run for hours after "battery low", probably/perhaps locking the percentage at 5 or something..

It's not an entirely exact science.. A battery's capacity is rated according to standardized constant current or constant power discharge tests, after a standardized charge to a specific voltage. The discharge test is terminated at a specific voltage too. This gives you a capacity number.
However, if you redo the test at higher load, or lower load, you get yet another set of figures. If you let the battery sit unused for a year, you get different results again.

On my N810 where I can actually measure power draw, and integrate over time, I've found that the "useful" capacity of the battery, as in the actual power you can take out of it before reaching battery low, varies by about 200mAh depending on whether I just chat on IRC or if I listen to netradio..
IIRC when I measured power in and out of battery with the charger connected, took the sum and integrated, the charge level of the battery varied by about 7 percent. With the device sitting idle.
If I launched netradio, with the charger still connected, the charge level would drift even lower. It would, of course, still claim battery full itself despite battery in reality sitting at around 75 percent.

Another interesting observation, charging seems to slow down when I use it. And I mean that it draws less power from the charger, not that less power is put into battery because device is using more.. Kinda counterintuitive behaviour really..