the three deep system came from and goes back to dr. basil furgala's research and practice (which dr marla spivak adopted), known as the 'horizontal 2 queen system", not sure why it was called this. many variations have developed since furgalas research and practice of keeping bees in 3 deeps. well worth a google, or to read up on furgala's research and practice.
the 3rd deep is not for the purpose to harvest, it is left on for the queen to lay up in, and honey stores left on for the winter. in my own experience of running a three deep hive, you must have a young vigorous queen or a vigorous queen to lay up in the third deep. managed properly, and in a good flow, one can get a good honey crop from medium supers, and the bees pack away the honey in the third deep as is said to 'maximize winter survival rate'. i don't know that this is always true, my own success rate was hit and miss. your queen, your flow/weather will be the key to success barring any other problems.