Not always waste. There are some important collections of atoms that you would prefer to move whole from one place to another, rather than creating new ones on site. Especially since it takes 18 years or more to do!

Other than that, I agree. Home nanotech for everyone!

Then again, nothing is more wasteful than producing everything locally.

Costs are comparative and opportunity costs.

What are the alternatives of transport mode A to transport mode B?

What are the alternatives to transporting inputs, outputs, and/or wastes?

Per ton-mile (or tonne-km) nothing matches marine shipping. The alternatives to shipping entirely might merit consideration though.

And induced consumption (shipping of X is now so inexpensive that consumption of X increases manyfold), a/k/a the Jevons Paradox, is another major factor.