MXsports is exactly the same as Disney, if they can find anyway to make an extra dollar they will take advantage of it.
From what I understand on Red Bud's website, if you are registered as an alternate, you show up on Friday and pay your gate fee and $25 to practice. On Saturday, the first race day, they wait until track registration is closed and if they don't have a full gate, they tell the alternates to come pay and line up. I think what is confusing everyone is the yellow and green check marks on the mxsports site. I believe one just means you are an alternate and the other means they have received your qualifying money. Red Bud's website states that the only people that can race that weekend are actual qualifiers or registered alternates, and the deadline is a week before.
As far as racing multiple area qualifiers, I can see in some instances where it is needed. I know that my son raced the Malvern qualifier and in his first moto a guy wrecked a hundred feet out of the gate, took an immediate left, and wiped out five other riders, my son being one of them and had his bike end up on the bottom of the pile. Although he made up a lot of ground, not enough to come close to qualifying. He qualified in his other class that day. We then went to another area for him to try to qualify, which he did.