I believe that your intuition is sound. I am also learning about CPT symmetry.
The CPT transformation turns our universe into its "mirror image" and vice versa.
The implication of CPT symmetry is that a "mirror-image" of our universe — with all objects having their positions reflected through an arbitrary point (corresponding to a parity inversion), all momenta reversed (corresponding to a time inversion) and with all matter replaced by antimatter (corresponding to a charge inversion) — would evolve under exactly our physical laws.
This means there is a distinction between a universe such as ours that is predominantly matter and its "mirror-image" that is predominantly anti-matter. However, we can't tell which one we are in. Granted, there would be such a pairing at every point and every plane containing that point. Still, there is a sense in which we can speak of two mirror universes.
Given that both possibilities are equally valid, shouldn't we suppose that, in fact, they are both true? Consequently, it would be straightforward that there is no reason for matter-antimatter to be balanced in a single universe, as it is balanced within the pair. In other words, it would be expected that one universe would have a preponderance of matter and the other of anti-matter. Whereas the Wikipedia article on charge conjugation raises a false problem:
The C-symmetry is particularly troublesome, physically, as the universe is primarily filled with matter, not anti-matter, whereas the naive C-symmetry of the physical laws suggests that there should be equal amounts of both. It is currently believed that CP-violation during the early universe can account for the "excess" matter, although the debate is not settled.
I suppose that it's much less presumptuous to suppose that there are dual universes, one of which is mostly matter and the other anti-matter, rather than to suppose that there are dual possible universes, one of which exists and the other not at all. The latter is like presuming that there is no back side to the moon if we haven't seen it. It's a general principle of quantum mechanics that all paths are taken, that all possibilities are true.
One consequence of your intuition is that we would not have to invent mechanisms to explain why a balanced universe doesn't have all the matter and antimatter annihilate, or to explain the observed imbalance. A more physical consequence is that if we suppose the matter-antimatter imbalance from the start, then the parameter expressing that imbalance can be a key ingredient in models of the unfolding of the universe. Indeed, if we suppose an imbalance from the start, then there may be a natural value for the degree of imbalance. For example, if we studied random matrices with n real eigenvalues, n odd, so that the number of positive and negative eigenvalues naturally differs, then we can calculate the likely distributions of the eigenvalues.