It looks like you need to set up automation for each stop individually. Ugh! Hopefully I'm wrong about that!
Recording all automation including individual stop enable/disable is working for me in Cakewalk by just clicking on one button, I suppose every host has a way of doing it with VST3 plugins somehow. But how do I do individual stop selection via MIDI? My PC monitor doesn't have a touch screen and I can't really use a mouse whilst I'm playing. Well, I think Cakewalk has some limited facility for this, and probably other hosts have ways too, but probably not enough for all the stops. I could also do it by making some modifications to my control surface plugin (isn't open source great!), but that option isn't open to everyone. The player should allow the use of RPN/NRPN for stop selection. Or the computer keyboard (the typing one, that is) itself. Just look at how Hauptwerk does it for some ideas.
BTW, you can easily find the stop number by double-clicking on the manual name (underneath the Play/Combine/Mix section) - the stop selection panel for that manual will then expand and you can see the numbers. However, the stop numbers as presented by the player to the host are sequential from 1 to 120, and they don't map one-to-one onto the stop numbers shown in the player. For example, say I enable "stop 80" from my DAW - that actually maps onto stop 116, Soloflute 4' in the player. So, I could write down the mapping, and even implement it in my control surface plugin so it shows the correct names if I really wanted to