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#231
Well, maybe because "empty" space doesn't have to mean that is all zeros, Even when a file is deleted data is still there but invisible to system. One good use for cloning is when you have to salvage data from a damaged drive. By cloning it to a healthy disk, all that data is transferred and there are better chances to salvage it with programs made for that. If you try to salvage it from original, damaged disk it may fail completely before it's finished because it has to work very hard during that process.
On the other hand, when you clone it, it stay as fragmented as it was on original, while restoring from backup its all contiguous except for reserved blocks.
All of that goes for any program for those purposes, not only MR.