West had 3 groups and 3 LMX teams. Central had 4 and 4. South and East both had 4 groups and 5 LMX teams. So we actually had an above average chance of facing LMX teams in knockout. It is just random that we end up in a bracket with the first 2 possible games being East teams we play all the time.
But it's bad that if we play Atlas again it would be in the Quarterfinals. Standard Tournament seeding puts the 2 teams who survive each group on opposite sides of the bracket so they cannot meet again until the final, which is always unlikely, but if it happens it happens. But they are committed to limiting long travel because the entire knockout is one short rest after another. And that is a function of your gripe: playing the entire tournament in a time period that is too short for its own purposes but too long for the problems it generates in the regular season.
They're just trying to do too much.
It's kind of ironic because Burki said this right after St. Louis got eliminated and now have 3.5 weeks off. But for teams who advance even halfway through knockout they added 6 games to a 34 games league schedule, plus USOC and for a few, CCL. It's too much. I fear MLS will drop USOC, which would suck for reasons of tradition and history and also not solve much because it is the least intensive element of the crowded schedule. IF MLS does drop USOC my Leagues Cup hatred will reach new levels.