"with the top two jumpers from each race progessing to the next course."
Won't it be unfair if someone gets top 8 time but gets third on his race and gets disqualified?
It would be unfair but that's the whole point of making people race in groups. You play against your direct opponents instead of everyone. But as HappyCamper said it would only be a problem if all the best jumpers end up in the same group on the early stage.
Tournaments normally deal with that kind issue with seeding: a common setup for 1 on 1 matches, for say 16 players, is to have seed #1 vs #16, #2 vs #15, etc. Another common thing is top 8 is randomly assigned an opponent among bottom 8. This is to avoid having the top seeds play each other in the early stage. Upsets are still possible but less likely, and the later stages are normally more competitive.
I'm guessing seeding based on submission times will be used to balance the groups. Also if i'm not mistaken the map was built with 4 jumpers per stage in mind, as there seems to be 4 timers per stage.