Honestly, some of the sources as to “when” to do an advanced spindown are mixed and the advice to only do it if they say so, is more to cover their asses.
Only thing that I can foresee going wrong, is that if you suddenly jam on the pedals while the electronic brake is actively shifting quickly, that it could over compensate.
There is no switch or sensor inside the device to “break or not break if wahopo gave permission”.
It’s a fairly simple process, it puts you through a short warm-up, and you spin down twice, once measuring the system friction, and the other measuring the brake strength. And some sources recommend doing it after moving where a trainer is, as well as when you first set it up.
I am an advocate of both, since I have seen many of these be off from the factory once they get installed in our homes.
Mine under reported, a friends over reported, and a third one was bang on, so 2/3 needed adjustment
That all said, if your favero is properly calibrated, then you could just use the pedals as your source with power match and be fine with consistent numbers inside and out