A permutation group is innately transitive if it has a transitive minimal normal subgroup, and this subgroup is called a plinth. In this paper we study three special types of inclusions of innately transitive permutation groups in wreath products in product action. This is achieved by studying the natural Cartesian decomposition of the underlying set that corresponds to the product action of the wreath product. Previously we identified six classes of Cartesian decompositions that can be acted upon transitively by an innately transitive group with a non-abelian plinth. The inclusions studied in this paper correspond to three of the six classes. We find that in each case the isomorphism type of the acting group is restricted, and some interesting combinatorial structures are left invariant. We also give a fairly general construction of inclusions for each type.