I'm not sure it's right to characterise Deep Blue or Stockfish as repositories of human chess theory. Fundamentally they were all based on a relatively simplistic function for calculating the value of a board position combined with the ability to evaluate more board positions further into the future than any human possibly could (plus a database of opening moves). That approach seems thoroughly non-human, and represents a victory of tactical accuracy over chess theory or strategy.
However I agree that the games between AlphaGo and Stockfish are really interesting. It strikes me that the AlphaGo version of chess looks a lot more human; it seems to place value on strategic ideas (activity, tempo, freedom of movement) that any human player would recognise.