I wouldn't say you are wasting space, but you could get more plants in the same space if you wanted to.
On the tomatoes, it is important to know that if you are only going to give them 1 sq ft, you need to be 1) giving them something to grow up on and 2) pruning the crotch suckers regularly -- otherwise they need about 4 to 6 sq ft of space.
The subject of the book 'Gardening when it counts' goes into why he recommends spacing plants out more. It has to do with root competition and watering needs. With intensive methods like square foot gardening, I think you are giving up some production, plant health, and have to water more than if you spread them out more. BUT, you get more plants in the same space, more diversity, and probably more food overall.