If I remember right, by default, trainers should use the themes associated with their trainer class in Rounds 1 and 2 or the default battle theme if they don't have a theme associated with their class). If you want to remove theme theme from Round 3, just delete the following line of code in 002_CoreSystem.rb
Code:
$PokemonGlobal.nextBattleBGM = "B2W2 212 PWT Final Round!"