I think the article fails to cover a lot of areas where Amazon will have a competitive advantage over UPS and Fedex. First of all, Amazon will be vertically integrated. They can control the packaging. They can control which warehouses are used to store items. This could lead to better packing efficiency in delivery vehicles, and could make automated loading of vehicles easier. If you have a particular route that is usually 110% full or 40% full, you could either move more items to that warehouse or take some away. Plus, Amazon can incentivize cheaper shipping options dynamically. Will the marginal cost of this order be incredibly high because you'll need a second truck for a particular route? Discount one day shipping, or offer two day shipping to their work instead.
On top of all that, Amazon doesn't have unionized employees. That's a huge advantage when you are trying to reduce costs. Not only are their employees wages probably less, but they also don't have contracts that reduce planning ability, like fixed routes, etc.
(The above is my comment on this post yesterday, though the post failed to get traction. I think it's probably still relevant 24 hours later)