It is possible to control organ stops and manual changes from within Dorico, as I have detailed on this forum thread, which is for Organteq. I was thinking about making a similar map for Hauptwerk, especially if there’s interest. (I have the old version of Hauptwerk, which was free for personal use, but I don’t think it’s available anymore.)
I may update that thread with a better expression map, or create a new one that includes Hauptwerk. (I can no longer edit the original post however…)
For manual changes, you create playing/playback techniques for each manual (e.g. I, II, III; or Gt., Sw., Ch.; or G., P., R.) which are mapped to absolute channel changes.
For stop changes, the basic idea is to (for each stop) create an “add” and a “remove” playing technique, each mapped to an add-on playback technique that fires a corresponding CC event. These techniques must all be placed invisibly on the Pedal staff so that they are all on the same channel.