It is easy to under estimate just how much better and more rigid a design like that really is. That is a really well thought out design. Much lower torque load on the gantry and it removes the wobble inherent in fixed table designs.
I completely agree with your idea of a double supported Y axis and moving table. This also lets you add a few more pieces and brushes to gain a semi - enclosed routing area.
The only location that I wonder about is the inside of your box structures on each side of the moving table. Since all of the Y motion is being transmitted through these boxes to the actual table, it might turn out that you can stiffen the design even more by putting some kind of cross brace diagonal inside the hollow box.
Of course, that is just MHO.