To sum it up a subtraction method needs to be added/replaced to the code on default instead of the ignore active topic count if there is a private forum.
I'm not complaining...I just like the feature and would like it to work on default even if there is a private forum.
I've been searching for a topic where this was discussed (haven't found it yet, but I'm pretty sure it was added during the v3.4 development stage). I do remember discussing this sometime in the past. It was probably done this way to either reduce database queries, or to simplify the code (or both).