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Not sure what your question is..
power level is the same for extended batteries and OEM batteries. They just last longer so ideally, the percentage will decline at a slower rate. But the max capacity is still 100% no matter what battery you have.
On my atrix, last time I flashed a rom, I meade sure It was at 100% charge then left it an hour. Went into recovery mode and wiped the battery stats (you can do that with a battery calibration software as well). Then useed the phone as normal and let the battery fully drain until the phone shut down by itself, then re-charged too 100% and then some minutes, now I can remove it from charger whenever I want and the reading is pretty accurate.