Correct, a top ranked farm system will probably produce more major league stars than the lowest ranked system. No, not shocking, so we should probably stop presenting it like we invented the concept of number "one" being a good rank to have.
I don't think we should disregard prospect rankings "because many will bust". I think they should be seen more as a snapshot in time of individual player pedigrees, and not of the system as a whole. We just graduated 3-4 top 100 prospects, which makes the system ranking take a hit. Our top pitcher was injured, another needed work on his mechanics, while a third prospect played across 3 levels and didn't mash at the highest level he attained. That also was a hit to the ranking. 4 other starters just had TJS that delays their careers for 18 months. Another hit.
Did our minor league system suddenly become bad? No. Did Schultz, Hagen Smith and B. Monty suddenly drop off and are no longer considered prospects? Of course not. But because of the nature of ranking systems, they need to look at healthy, pedigreed dudes who are dominating their current, age-appropriate level, and declare who has an elite system from that.
Is it unfair? I wouldn't say that. We just drafted an elite defense shortstop who could be a stud if suggested hitting tweaks are made. We also plucked an elite high school bat that will also rank once he produces at any level. But their true potential remains to be seen, so that's a drag on the overall ranking. Every other system experiences the same ebb and flow, so a #19 ranking has so many moving parts.
Colson was dropping, but he just put up 3.3 bWAR in less than half a season. To paraphrase another poster, here, minor league rankings don't win World Series. Players putting up 6 WAR seasons in the majors do.