Prop-
When I did my rank list (with categorical, advanced and prelims), it told me I had like 23 "ranks" certified (including my prelims) but then only listed 17 or so "programs ranked". Not sure exactly how they delineate the difference between the two, but I'm guessing they're not counting my supplemental rank list against my 20 program limit.
Also, I was led to believe that if you went over your 20 programs, you had to pay extra RIGHT THEN to certify those extra programs. They even made it a point to say that if you then take programs away later, you don't get the money back. As I didn't have to pay any extra money to certify my list (with the 23 "ranks", I can only assume that I'm only being charged for the 17 actual Categorical and Advanced programs listed on my Primary List.
I have no idea about how the Scramble would work if you listed a prelim position on your Primary List and then matched there. If you want to know, I would e-mail Student Affairs (or a CERTAIN chair of a CERTAIN department) and see what they say (but knowing you, I don't think you need to worry about that).