MusicBee does not have what you called a "smart gain mode" when analysing tracks/albums and writing ReplayGain values to them.
And that is the first and most critical step that will be defining what will and can happen when actually playing the music.
Also, since you are posting this in 'Bugs': what is the "verifiable bug and malfunction" exactly?
To me it seems like you may have some sort of suggestion or request. (which are usually valuable and appreciated)
Check the already outstanding wishes on similar matters regarding ReplayGain and clipping.
Support them, or add a new one on the Wishlist board if you can't find one that voices what you are asking for here.