These accusations of unfairness in a round-robin to a flight cut format (eliminate teams from certain spots of contention) seem very much overstated. Is seeding important? Yes. Does PACE place a lot of emphasis on getting the seeding right? Yes. What's the problem there?
More to the point, however, why are you holding up HSNCT's system as some sort of golden standard of being able to upset teams and place higher? (note: I'm of the opinion that the HSNCT format is good and that there's no real point in comparing it to NSC). Each format has its own unique pluses and minuses.
If you want to get technical, you've got a better chance of punching above your weight at NSC because one key upset can change your minimum place by 24 spots -- you don't need to win a series of games. No one criticizes the NSC format for this because it doesn't square with the empirical results of the format as used at numerous tournaments every year and a significant number of NSCs in particular.
Plus, let's take a look at
the HSNCT stats. If every team took the above attitude, fully half or more of the 53rd and 77th place finishers must be livid that worse teams* such as Homestead B and Stevenson B had the gall to finish above them. AMSA and High Tech and St. John's must feel cheated that a number of 13th place teams above them are worse*. Hinsdale Central must feel really cheated because all of the 5th place finishers are clearly worse*. Why, LASA must feel the most cheated of all: their field-leading 452.3 PP20TUH outclasses TJ by 87.1, their field-leading 23.54 PPB leads TJ by 0.82 (a quite significant margin at that level of PPB), and they even beat TJ by 300 earlier in the playoffs -- NAQT should've just replaced TJ* with LASA in the final! (fun side note: I almost guarantee that you can crown a 200th+ place finisher the champion of HSNCT by following a simple transitive chain of Hunter lost to A who lost to B who lost to C who lost to... Z. Is this team the true HSNCT champion?)
*purely by looking at stats of course! I'm not saying your team is actually worse -- I'm simply using the same method of analysis as above.