This isn't a knock on the Scottish Rite ... but I wish someone way back when wouldn't have assigned numbers to the degrees. That is where a lot of confusion arises, especially with people outside the lodge. Just because 32 or whatever is numerically more than 3, they think it is "higher."
I love that picture from Life magazine about the structure of Freemasonry. In fact, it has been the desktop background for years. But, as we have already said, it gives a false impression. The Master Mason degree is almost lost in the picture. The most accurate chart would have the MM at the top with the YR and SR branching off to the right and left.
I don't think there is so much confusion with the YR degrees because the degrees go strictly by name and not given a number. If you wanted to assign numbers to all the YR degrees (because the Blue Lodge is considered part of the YR) and know the true chronology, it would go like this.
EA - 1
FC - 2
Mark Master - 2.1
Select Master - 2.2
Royal Master - 2.3
Master Mason - 3
Most Excellent Master - 3.1
Super Excellent Master - 3.2
Royal Arch Mason - 4
The Commandery has Orders, not Degrees, and fall completely outside the structure.