What are the major advantages of the Late 2013 rMBP 15'' high-end model over custom configurations of its low-end counterpart? I mean other than what you can configure, like RAM and SSD capacity and CPU speed and the fact that the ME294 comes with NVDIA Graphics as well as the Iris is there anything else different? Like motherboard (logic board they call them?) features, or Chipsets on the board?    

To put it differently, I usually see similar laptops on Apple online store, with one model starting at lower price and if you choose more RAM/CPU/HDD on the lower end option it looks like you get to the higher end model, both price-wise and spec-wise is there anything else other that what meets the eyes to be considered?

EDIT: So by the looks of it, it is not just a matter of difference in RAM, HDD, CPU speed, that separates the lower end models from higher end models, they are really different things, in some cases it may be just a small difference, but in some it may be significant, I think I got my answer. From the comments.
And for the reference the models are like ME293LL and ME294LL
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.