Despite all of the great ideas that have been contributed to kit ships out to deal with squads the following flaws still exist.
A. The cost analysis that you are doing on Kallus, QLT, PDR, cluster bombs, flight controllers, etc does not take into account the opportunity cost of taking them. In most tournament situations, you are better off taking upgrades that are more general purpose.
B. Most antisquad upgrades, exempting cluster bombs, require that the ship have several activations in order to reap the full benefit of the upgrade. Fighter lists of 134 points run about (Imperial 8-12?)(Rebel 10-20?) of anti ship damage per round. This means that unless the intel allowing this is eliminated, ships are not going to be around very long.
C. The typical solution to A and B is to use ships that can use superior speed and maneuverability (through nav commands, meaning you can't rely on squads) to get a winning advantage. This approach is HIGHLY dependent upon some bombers missing shots and the non squad fleet not missing shots. I believe someone named Ard has an excellent testimonial to this approach someplace.
D. Are rebel squad builds unbeatable?, no. Are they some of the most consistent fleets to not lose by a bunch of points?, probably. I'm not trying to jump on any NERF X and Y trains. Merely trying to point out that there is a cold hard math to upgrade selection. In Armada fleet construction, its not practical to throw in 60 points of tech in upgrades(Kallus, QLT, et al) or squads(IG, Ewings, et al) on the off chance that you get to use it.
Also, as a random note. Watching elimination matches to analyze how a fleet performs is not representative at all. I realize that since that was the only round streamed, its what we have to work with. In elimination matches the game of Armada changes victory conditions. You are no longer looking to score lots of points, you are looking to score one more point(1st player) or tie(2nd player). This leads to a play style that is nothing like what swiss is played as.