Clipping is an extremely complicated operation. It is hard enough to implement it for triangles or tetrahedral elements, so I guess that’s why the mesh is converted to these elements before clipping. Maybe you could give it a try and implement clipping of cell types that are important for you in VTK. You could also add pedigree IDs to cells so that you can trace back which original cell each new cell corresponds to.
From the examples above it is not clear at all what’s happening - what VTK filters are used and how. If you would like to have VTK users or developers to look at a problem, then probably you need to provide VTK examples.