For running a sweep, there are two main requirements for the results to be merged:
- Matrices having same dimensions.
- The data being recorded for same coordinates (x, y, z).
Following a change in the structure, the mesh would also change when using the automatic mesh setup.
Therefore yes, you need to enable the override mesh option when sweeping to ensure that results are obtained for same coordinates.
Answering your second question, since the cells need to match across the structure, the mesh will extend out from the defined mesh object (in directions which you have enabled the mesh override for). Therefore, in your case given the geometry, you can expand your mesh object in Z direction so it will fully apply to your monitors (shown below).