In this paper, we theoretically study the influence of a non-magnetic spacer between ferromagnetic dots and ferromagnetic matrix on the frequency dispersion of the spin wave excitations in two-dimensional bi-component magnonic crystals. By means of the dynamical matrix method we investigate structures inhomogeneous across the thickness represented by square arrays of Cobalt or Permalloy dots in a Permalloy matrix. We show that the introduction of a non-magnetic spacer significantly modifies the total internal magnetic field especially at the edges of the grooves and dots. This permits the manipulation of the magnonic band structure of spin waves localized either at the edges of the dots or in matrix material at the edges of grooves. According to the micromagnetic simulations two types of end modes were found. The corresponding frequencies are significantly influenced by the end modes localization region. We also show that, with the use of a single ferromagnetic material, it is possible to design a magnonic crystal preserving properties of bi-component magnonic crystals and magnonic antidot lattices. Finally, the influence of the non-magnetic spacers on the technologically relevant parameters like group velocity and magnonic band width are discussed.