From v8.5.0, when a note adopts a prototype, the note's $Height and $Width are initially changed to match those of the prototype. However, this is a one-time effect $Height and $Width are not inherited; the change affects only the initial dimensions of the note.
From v8.6.0, when assigning a note to a new prototype, the note's initial $Height and $Width are set to match the prototype's height and width provided that the note's dimensions have not already been changed from the default. If the note has been resized, those dimensions are now preserved.