The way to solve the “different difficulty level randomness” would be to stop pairing people based on equal prestige, and start pairing people to try and equalise SoS.
So after each round, you’d run some kind of algorithm to pair people so that the “current SoS + prestige of next opponent” was as equal as possible across all participants. So someone that had been playing hard opponents so far (high SoS) would be given an easier match (lower prestige opponent). It’s a fundamentally different principle to what we have at present, with a different priority. You would get more lopsided matches but every player in the tournament, from winner to wooden spoon, would have faced an equally tough challenge over the day.
If I was in charge, I’d run tournaments so that there was a clean cut by design. Everyone who shares a record with nth place gets in and high seeds get byes to make the tournament work. SoS is then only used to determine seeding, which is much harder to be unhappy about. As it is, I think we agree that weighted SoS makes no sense, and that needing tie breakers makes some people feel hard done by.
Using a bye requires earning that bye. So, to get those round 1 points you have to win an entire tournament instead of two games of Netrunner. Usually this is substantially harder, not easier