Yeah I'm also used to the ranking of S being superior to A class.
The, C, B, A, S ranking system is almost very similar to the whole: Bronze, Silver, Gold, Platinum ranking.
I mean ignore anything you know about Platinum for a moment, and one would assume it makes no sense for something random like Platinum to be ahead of Gold (something that because of lack of knowledge at the time, caught my attention), but I never knew why, so I just accepted. Curiosity got the better of me, and I found out Platinum is actually worth more than Gold, so then it clicked.
The S rank being the highest is pretty similar, in that it likely means Superb meaning top of the class, you succeeded in doing better than A. Sure maybe the whole F, D, C, B, A report card gets you confused, but if I remember correctly, S's are used in Kindergarten (or maybe higher, can't remember the grading system they used in Elementary School) as they rank your skills in certain areas of learning. So I'm used to S's being the highest grade possible, though I can see how the whole school grading system in the later years can get you confused.