Hello Kenneth,
To my knowledge, all commercially-made digital/electronic organs use matching MIDI input and output parameters for their stops (intentionally so that they can be recorded and replayed via MIDI sequencers). That also has the major benefit that auto-detection can configure them automatically, both for input and output, which wouldn't otherwise be possible.
The Hauptwerk user guide strongly recommends that the same approach be adopted if building your own do-it-yourself console, for the same reasons. As far as I know, all commercially made consoles designed for Hauptwerk do adopt that recommendation.
If building a console yourself, then why not just follow that recommendation? It wouldn't normally add any cost or complexity to do so. Have you built a console yourself that doesn't do that? If not, could you not reconfigure the MIDI encoder/decoders appropriately?
(I appreciate that it would, for example, technically be possible to implement translation tables to remember mappings for each given MIDI switch so as to re-use the mappings when auto-detecting that switch again, and/or to add macro/scripting ability, etc., but those things would be significant amounts of work to implement and add considerable technical complexity both internally and for the user. Surely it's better instead just configure the MIDI encoders/decoders appropriately in the first place?)