What the other tools do
Most commercial tools have one or two channel mixing capability. Which means when you paste a WAV clip onto the channel it is immediately mixed in. This presents problems if you don't like the starting location or the volume of the sound effect on the channel as there is no way to split it outother than an undo feature and then trying it again. SoundEffects keeps all the wav files separate and mixes them only to write out the file or play them back. So each wave object can use an independant volume and starting position within the final WAV file. This allows the tool to let you grab sounds with the mouse and manage them independantly on the channel.
Ever notice with one of the standard tools that your sound starts loosing quality the more you play with the volume control? That's because the data is continuously being recalculated and overwriting the master. With SoundEffects, because the WAV source is kept separately from the mixed source, the volume calculations always occur from the original master, resulting in the best possible sound.
The downside to all this recomputation is that you need a hefty PC to be able to handle the load, but if you can play FreeSpace on it, you won't have any trouble.