The Commuter fits with the extended battery just fine (At least on the GSM phones, I don't know about the Verizon/Sprint version). It's not the PERFECT fit with the stock battery and door, but unless you look closely you'd never notice.
The case is designed to fit the shape of the phone with the stock battery door, which means it follows the taper of the phone. With the extended battery and door, the phone has a slight bulge instead of a taper. What this means is that for me there is a slight gap between the outer shell and the silicone inner part (roughly 1/32 of an inch) near the bottom of the phone. With the stock battery cover this gap isn't there. It does not in any way affect the use or the protection of the case, just affects how it looks. And really, unless I look directly at it, I don't notice it for day to day use. I only tell you this in case you have OCD and something like this would bother you. (I have touches of OCD myself, and it doesn't bother me)
I can take pics if you want to see the difference for yourself.