Guilin Sun
Ansys Employee

I personally do not recommend using many override regions. You can simply use one override for the rectangles, and use auto-mesh. This not only greatly simplifies the settigs it is also easy to maintain and modify. The two designs are not the same since they do not have the same geometries, at least in discrete mesh space. Please refer to 

1.       Understanding Mesh Refinement and Conformal Mesh in FDTD

2.       Understanding the non-uniform mesh in FDTD