Only type of squat that may come close to upright, with good form, would be a by-the-book BB'ing squat. Bar high up on the traps, chest out, stomach in and back/spine straight. Of course that never happens in the real world workouts, just in the men's & womens "fitness" mags or videos. The pure mechanics of squatting see's to that. If your a good, to excellent, squatter you back is not going to be completely straight.
Using a 2X4 (3ft long at least) under the heels, rather than BB plates, give a better foundation for squatting. The work load is placed a little more on the lower quads, while giving better balance when squatting. Also seems to reduce some of the stress on the lower back. Can use very heavy weight with confidence on this exercise, just as in regular squatting. I also use a 2X4, under my heels, for BB Hacks. A superior quad exercise, for me at least.
That "knees never beyond the toes" thing does not apply to everyone. Exception would be serious PL'ers. With Nodeal being 6'4, that is extremely hard to do. On the other hand, dwarfs may not have any problem with it at all. Learning the correct method of box squatting goes a long way in teaching how to get the most potential out of squatting. Though again, this is usually reserved for serious PL'ers.
Step-up's can come very close to having the knee's in line with the toes. Heavy lunges can also be included in this regard. With a Smith machine, you will be leaning back against the bar for balance, while squatting up. Knees in line with the toes. Some people like this method. Whatever gives success I guess. Good Luck.