The Alt Configs are literally "Alternate Configurations". You can only have 1 organ loaded in Hauptwerk at a time. You could set one config to always load Organ A as the default when first launching HW and another config to always load Organ B as the default. These Alt Configs are extremely useful for for switching between custom audio layouts. For example in a typical audio interface setup with active monitors: Config 1 could be four channel audio, Config 2 could be two channel stereo, headphones only. This saves having to turn off 4 speakers and maybe a subwoofer for private listening.
Did you know you can assign a MIDI key to a respective favorite organ? This may allow switching between organs a little quicker by just pushing a MIDI enable button or piston.
Danny B.