I think it will punish the human more than the bots cause the human normally play less matches and get less winstrikes.
Other point: Do you really think that it won't be possible for the programmer of bots to take this point in their calculation ?
F.E. many player have the chicken only at level 1 to have a non-melee chicken (what is in opinion not correct why I cannot put a max-level-chicken in a battle and the opponent can put his level 1-chicken ? - why I cannot use my max-level-chicken also at level 1 (or 2) ?) So one bot could submit the team with level-1-chicken and the other bot with level-2-chicken and it would doesn't matter that the teamorder is the same, cause of the different level of the chicken (also if stats of Level-1-chicken and Level-2-chicken are the same) the battle would start.
You are probably right, bots seem to have the competitive edge when selecting teams as they can program for more possibilities a human has time the think of.