I replaced the battery in my 2007 E90 328i about 7 weeks back. Called the stealerships in Houston and all of them wanted around $450.00 to replace and register the battery and the battery prices varied between $199.00 and $239.00 for the 720 CCA 90ah battery. With a 10% off parts coupon, managed to pick up the battery for about $197.00 (inclusive of taxes and disposal fee). With my car parked in the stealership parking lot (I live 60 miles away from the closest stealership), I removed the old battery and installed the new battery in about 20-25 minutes. Used the INPA cable with Toolset 32 and registered the new battery and haven't noticed any differences in the car.
A friend of mine had a $75.00 battery installed by a local gas station mechanic on his 2006 E90 325i and didn't even bother to register the battery. His car has been running without any issues for over a year now. Several others have installed Walmart batteries and haven't had any issues.
So, I'm not sure if the battery really needs to be registered but I did mine anyway with the tools I had at my disposal. Only time will tell if I did the right thing or not.