They don't. The characteristic flavor text points out the highest IV the pokemon possesses.
And that pretty much answers your other questions, I'd assume. ^^;
For example, your Rayquaza with 31 SA would be "Mischievous." That is, 31/5 = 6 r1, which is listed as such in the table.
To me, it seems like Nintendo keeps adding mechanics that make previously "hidden" stats more and more visible.