The main reason for a double Z-axis is that is achieves a balance between rigidity and usable throat depth. The problem with most systems starts when the system designer is going through the "what if" stage. "I know I want to cut aluminum plates but 'what if' I want to cut wood or foam that could be 6" or 8" deep?" And the first thing they do is jack the X-axis way up and then dangle the Z-axis back down to where they can cut the 1/4" plate they are mainly intending to use the machine for. The problem is that the leverage the cutting forces have on that long Z-axis arm that is dangling down creates flexure in the system and that flexure allows the bit to skip off the surface of the aluminum it is attempting to cut resulting in poor results and excessive heat generation. With the double Z-axis system, the X-axis can be kept low such that the Z-axis isn't having to reach for the material that is being cut which means better rigidity and better rigidity means better cuts. So basically the answer to your question is that it allows the machine to be at its best when cutting thinner, harder materials and gradually losing rigidity as you move up to taller, softer materials.
I would probably go with the C-Beam® Gantry Plate - Double Wide plates with 8 mini V-wheels each on the Z-axis. That'll give you the best leverage against both side sway of the frame and the outward rolling forces caused by the weight of the spindle extending outward from X-axis. Less rigid, probably not as you'll be using big honkin' C-beams for all the framing members as opposed to 1/4" end plates which can have a fair amount of sway when they get too tall. (Google "frame sway" for a better explanation.) The only potential sway will come from flexure of the wheel axes allowing some movement but I don't believe it will be anywhere near the flexure of typical tall thin end plates.
