What are the major advantages of the Late 2013 rMBP 15'' high-end model over custom configurations of its low-end counterpart?
A custom-built ME293 model with a 2.3 GHz CPU, 16 GB of RAM and 512 GB of SSD, although costing the same as the stock ME294, is not the same hardware because it's missing the Nvidia GPU. I speak from experience as I have one of these (Intel GPU only), with the 2.6 GHz CPU upgrade. Other than that I'm fairly sure they're identical.