It's not totally clear for me what does it mean "trying to sort the entire hr on the keys of layer 4 first and layer 3 second", but if it means to sort by the 4th column as the key and 3rd column as a subkey, then probably you wanted to write this to sort the flattened array:
sort { $a->[3] <=> $b->[3] or $a->[2] <=> $b->[2] } @flat_array
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