I agree, it would be best to have human vs human rounds all the time with a repechage mechanism after the first round.
Example nation with 200 users: round 1 100 go through and 100 lose. For round 2 you need 128 users, so 28 losers are randomly put back to the draw.
The largest nation is currently Spain with around 1500 users, it would mean a first round of 2048 teams (it means the cup would have 11 rounds). So first round 750 go through and 274 are randomly brought back.
The number of rounds remains the same though, so I agree it's probably just a bot removal thing.