The so-called alternate timeline is not actually such, but rather an alternate universe altogether. Neither universe was created by actions taken within the other, but have always coexisted parallel to one another. It is possible that such a universe is composed of mirror matter, or exists as the result of some other hypothetical concept in physics.
Nevertheless, certain actions taken within each universe can have an effect on the other, such as Juliet's detonation of the hydrogen bomb. The bomb's energy transfered to the parallel universe as a side effect of the electromagnetic pocket of energy. This lead to the Island sinking in the parallel universe. The existence of a parallel universe allowed Faraday's reset to work while at the same time preserving the Novikov self-consistency principle, more commonly referred to as "whatever happened, happened."
Furthermore, the Dark entity is originally from this universe, and it is to there which he is trying to return.