Thanks to this question I now understand that The Architect and the Deus Ex Machina are two different entities. Before, I always thought they were one and the same because of the last scene in Matrix Revolutions.
We know that the Deus Ex Machina makes an agreement with Neo and and in the last scene, The Architect says that he will allow those still inside the Matrix tro be set free and because he is not Human he will keep his promise(!). It always felt like he was the one making the deal with Neo because of that.
If The Architect is not the Deus ex Machina then why is the Oracle trying to get him to agree to free the people inside the Matrix? And if he isn't the top authority, how come he can make independent decisions on such a big issue?