Is this how the real world works? First of all, this machine is exaggerated as a description of the real world: even the most complicated flux compactifications we know only use a few ingredients all of which directly follow from the basic equations we can write down and whose co-existence is governed by the same, very accurate laws of physics.
But if you forget about this difference, you could still ask: can the world be based on similar redundant mechanisms that seem more complicated than necessary? I think that the rational attitude is to assume, in agreement with Occam's razor, that it is a priori unlikely but it is not impossible. One must always be ready that extraordinary evidence eventually justifies extraordinary statements and the results in flux compactifications are not so terribly far from this possible outcome.
There are many things that we already know are much more complicated than our ancestors believed. Who could have thought that the identity of a human embryo needed to specify 3 billion letters? Incidentally, when I was a kid, I remember reading a book that argued that a person who lives today could be genetically identical to an ancient Greek warrior: it could be his modern twin. Does it seem plausible to you? It seems impossible to me. There must be many more than trillions of possible humans.
Update: Jorge Pullin has reminded me that the best Rube Goldberg machine as of today was created by