Case Analyzer and Battery Analyzer are two very important processes that a mod maker must use while setting up and configuring the device. Those settings are specifically set to the device. Guessing at things like battery soft cutoff and etc. is asking for trouble. The device should have shipped after being configured properly by the maker. These settings would have been uploaded to EScribe the first time you connected it to EScribe.
The 3.09 V default in EScribe was/is the setting defined for the specific battery used in the reference device. It is not the default for any/all batteries from my understanding.
If your device didn't come configured properly for the enclosure (using results obtained after running the case analyzer) or battery (using results obtained after running battery analyzer) then the designer failed to properly configure their device and you should run both analyzers and set the device accordingly.