The problem is less that his suggestion makes sense, it is more a problem of implementation and subsequently of people expecting a certain behaviour which will be difficult to satisfy.
The midi file logs only changes, not the absolute state of the console (reason for that is that this is the most common and compact midi standard which allows you to easily manipulate your recording in the midi file during post processing). As such, I assume it would be possible to add the current registration at the beginning of the midi file. Depending on how this part of the engine is architected that might not be trivial though. That doesn't come without caveats either. As a minor one the initial recording would probably sound different, as on subsequent playback the stops would get set while on the first recording they just stay (the one time you get the stop actuation sample played, the other time not).
Once people see that the stops keep their settings, they will think that all settings are kept for a recording which I assume will be more difficult to achieve than just the exception for the stops.
I guess to avoid that it is simpler to simply cancel the whole registration in order to make clear that you have to apply all settings before starting to play.
I personally think that this nothing more than a nice-to-have, certainly not essential. It is simple enough to open up the piston toolbar, press "set" and chose one of the pistons to temporarily store that registration and subsequently deselect "set".
Please also see page 81 in the manual:
https://www.hauptwerk.com/clientuploads ... rGuide.pdffor details on this "work-around"
Best Regards
Mathis