Anything custom adds a lot to the price. Consider the size sheets of acrylic come in, if there is less cutting involved sometimes the tanks are actually cheaper.
Consider this http://www.fishtanksdirect.com/rectangularacrylicaquariums.aspx
Some examples:
230 Gallon Rectangular Acrylic Aquarium 72x24x36 $2,590.00
240 Gallon 96x24x24 Show Aquarium By SeaClear $1,535.13
300 Gallon Rectangular Acrylic Aquarium 72x30x36 $2,850.00
420 Gallon Rectangular Acrylic Aquarium 96x48x24 $2,819.99
Just a few examples of where staying with standard sizing can save a ton.
I realize this is a really old post, but in my search for a tank in this general size range it keeps coming up on Google so I feel compelled to respond to it (in case others are searching and reading it too). The two examples you have listed above do show differences in price / gallon, but the main reason is not because they are standard sizes, it is because taller aquariums need thicker materials and are thus more expensive. Your two examples are both comparing a smaller 36" tall aquarium with a larger 24" aquarium, but in both cases there will be more acrylic used in the smaller (but taller) aquarium.
Sorry for bringing back a dead thread for something like this, but as I said if you type in 72x30x36 aquarium (which is what I'm looking for and researching vendors / filtration strategies / backgrounds, etc) its one of the first hits on google.