It never came to my mind that one could understand this as a recommendation against the SF update function. Maybe it would be wise @jovirkku to give an extra hint here although the documentation looks good to me.
People tend not to use the normal update function for good reasons and also based on rumors and misunderstandings.
Emphasizing the normal update process a bit more might help.
Edit: @Seven.of.nine and @atlochowski just brought a similar issue up:
https://forum.sailfishos.org/t/q-how-to-make-update-from-4-4-0-58-to-4-4-0-72-correctly/13175
And we had a discussion on update methods in the German section