I wouldn't call it the worst way to draw -- these studies are excellent at training the eye to understand things as they truly look (rather than the shorthand symbols we are accustomed to), but would agree that one will find their ability to draw from imagination extremely lacking if studies from reference are the only exercise used. An understanding of construction in 3D space is fundamental to the creative aspect of drawing.
There is an exercise in "Drawing on the Right Side of the Brain" where you turn a photo upside down and try to replicate it. Turning it upside down is specifically to prevent you from knowing what you "should see" so that you can better focus on what you actually see.
When I observe people who quickly paint portraits, they usually first fill the paper with big dark areas (where the major shadows will be), and only afterwards add shapes and details. So it's a bit like iteratively loading JPEG: first the entire picture in low resolution, then gradually increasing resolution.
Would you call both these approaches "learning bad habits"?
