strmxor -u|-deep (hierarchical xor) is marked as experimental, but is working well for the testcases I've tried.

Unfortunately it creates rather large result files due to the fact that it keeps the full hierarchy with all references.

strmxor --drop-empty-cells will solve this. This is an option only visible using --help-all.

For a P&R block with some changes, the result file size differences is rather large:
55MB vs 88KB for the same result polygon.

I would argue that --drop-empty-cells should be the default behavior.