It depends on what you want to do. If you want a totally customized mag, then it doesn't pay to buy a base model and upgrade. You won't be using very many of the stock parts, so the cost wouldn't be worth it. If you buy a partially customized mag that has many of the parts you need, then most of the parts will be used in the new build and the cost will be significantly less than buying each individually. The good news with mags, is that the parts usually have a long life span, so buying used is not as much of a problem as with other markers.
Except for the Automag in front, its usually the man behind the equipment that counts.