God has many aspects. Purely : Life - casual process. Implementation of casual process - is casual only for its participants. Defining specific values of random variables it is possible to implement any the scenario... I.e. God (programmer) along with a set of "physical" laws of a reality created also the mechanism which allows to supervise a row, without making miracles.
About a matrix: Yes, years through 1000 in what Space Studio any schoolboy on can create the virtual Universe, selecting from the menu system of consistent laws of the nature, to create there ten another of the worlds occupied unstable, evolving with "reasonable" beings and to watch process of evolution of consciousness and spirit, technics etc. As for stability system should have back couplings from the future in the past (differently it spaces simply apart) besides nature laws there are also the local "deities" implementing the purposeful scenario of development.
I.e. there Should be certain "DNA" of an organism of Mankind which leads to that it reaches a certain integral state. Here the cellular analogy is pertinent. All cells of a human body live the destiny is a colony of cells. Any cell does not know that such the person though has the target information on its structure, up to some singularities of behavior defining destiny (experiments with twins living separately). Process of formation of an organism from deckman cells - too some kind of a miracle. I.e. in ourselves, probably, the program of formation of "Mankind" as an organism, but we cannot experience it is put also, yet we do not master mechanisms of self-organizing of systems such as a live organism. Moreover - any cell of the person does not know that the person for what he exists wants - he lives absolutely in other world with other senses. The mankind as an organism - too has the semantic environment which is distinct from level of people until people do not break some barrier.
Realization of can become such barrier, for example, that all laws of the nature are fulfilled on some "computer" and that it is necessary not only to study laws, but also to master the computer that allows to quit on level of God and to start not only to control nature laws, but also to quit on level of "creators" - for limits of the Universe and the computer in which it goes. Well it as virtual "mankind" it would master that computer on which "goes", would start to rewrite programs and to communicate with us not simply as equals, but probably and would teach us how to "break" our computer or it would make, leaving us as the tool creating physical computers in our world.
It is clear that for modeling of the Universes the present quantum supercomputers are necessary...
Adding from 12/4/2016 08:54:
On the other hand, creating the Universe it would be desirable to use model on a maximum, instead of to implement a certain unique scenario. I.e. probability density of the unique scenario ~ 0, hence statistical value of the unique scenario is close to zero. Means for learning of laws it is necessary to launch family of the parallel worlds different by rows, but corresponding to criteria of stability if we do not set as the purpose learning of the end of the world that deserves separate family of models...