From the user manual...
You can quickly choose a fadeout ending, just press the [Fade] button, and Band- in-a-Box will fadeout the last “x” bars of the song (you can specify how many bars). Or customize the fadeout with precise values for each bar.
I believe that implies that it does not include the "two-bar ending". It's not a setting to "fade for x number of bars after the end of the song", but a setting to start the fade "x number of bars before the end of the song". That's how it works.
I would suggest turning off the two bar ending, enter a hold for the ending, and start the fade appropriately.
If you would like some different behavior, you probably need to visit the wish list, but don't expect immediate gratification.
Alternatively, use Realband (or another DAW) where you have full control over the entire volume settings.