Apologies, this is now looking like a mind dump, but writing the previous post I had an epiphany and changed the order of my filters. The reason why ghost cell generator filter wasn’t active was due to multi-block data structure of my data source. Now my filter order is:
MergeBlocksGhostCellGenerator-
CellDatatoPointData(with Piece Invariant checked) ContourConnectivity
And it produces good looking surfaces.
Please advise if you think this is still somehow inefficient or may cause issues with accuracy when a number of objects increases substantially. Otherwise, I hope someone may find these notes helpful.