There is no functionality in MusicBee that can store something such as 'pause play for x seconds after this specific song has played'.
Your best bet would be to edit the songs in a tool such as Audacity and add the duration of silence per track to your requirements.
Or, if your user case is related to playlists, you could create a couple of silent tracks with different lengths (2 seconds, 3 seconds, etc.) and see if you can place them at the desired positions in your playlist.