You would use your own e-commerce software rather than a ready-made one for uniqueness, specific requirements, a client requests it and as the author Michael Peacock points out, familiarity. That is once you create a framework that you have intimate knowledge of it is much easier to extend, improve and customize it.
Amazingly creating a PHP e-commerce application, especially with such well written step by step instructions, is nowhere near as time consuming or technically challenging as you might have thought. And remember when your done the advantages mentioned. You would just have to add a few unique features and a template and each client has their very own, custom made for them e-commerce store.
That has got to be worth allot in todays off-the-shelf dominated market.