You still confuse methodological materialism with the philosophy of materialism. Science utilizes methodological materialism. This means that science must study the universe as if no supernatural phenomena exist. That is not equivalent to the statement that science must assume that no supernatural phenomena exist. It simply means that if there are supernatural phenomena then science has nothing to say about them. For example, evolution states that the vast diversity of life arose from the processes of genetic variation (through several mechanisms, including but not limited to mutations) and natural selection. It does not say that this process was or was not guided by God, since science simply cannot deal with the concept of God. In this respect, science IS compatible with theism. Scientists need not assume that God does not exist; the existence of God is an open question as far as science is concerned. Science, in fact, is most consistent with the doctrine of essential agnosticism. Unlike some agnostics, who believe that there is insufficient evidence to determine whether or not God exists, essential agnostics believe that it is impossible in principle to ever determine whether God exists. That is the view of science in general. Individual scientists are, of course, free to believe as they wish.
You can explain the workings of an internal combustion engine without resorting to any supernatural speculation. You also know that GM, Ford, Honda, etc., built that engine by the fact that is inside a Chevrolet, Ford, Honda, etc. vehicle and has a VIN imprinted on the engine block that identifies the manufacturer. If the natural universe can be likewise explained entirely without supernatural speculation, and if there is no indication of any creator, as there would be with an internal combustion engine, would it not be more reasonable to assume that the universe has no creator? The theistic scientist would then be holding to a contradictory position: accepting the picture of a universe that provides no evidence of a supreme being yet believing in such a being.