You cannot live IN the matrix, but only UNDER the matrix since it is an UR-SOFTWARE that controls all hardware and inferior software and in this controlled universe of hardware and software, human beings are nothing but hardware pawns of a special nature: they can rebel and they can commit suicide. But Yes you are right. We are living UNDER the Matrix and this Matrix is the Architect himself and his human appearance at the end of the trilogy is nothing but a visual phantom for the two witnesses who do not want to believe they are nothing but specks of dust in a cosmic blender.
Each one of us has to go through a rite of passage with two questions: where to? and what or which rite? And no guarantee it will work. Tomorrow is just one more day like all others before and probably after. That's the real Malthusianism of life. We cannot stop the durable and sustainable existence of the cosmos in which we are a speck of nothing lost in a flood of other specks of nothing, and we have no power over this flood. Our sole chance is that we can more or less make our immediate space around the speck of nothing we are cozy for us and protective as for against other specks. The great honor of such a life is that it is moderately durable (it has an end) but it is not sustainable: it implies our own self-destruction added to the cosmic destruction we are living within.