That concept is excellent since it will have good stiffness for forces parallel to X and excellent torsional stiffness.

In case you've not already spotted it:
http://www.mech.utah.edu/~bamberg/re...e%20Design.pdf

I'd probably stick to using one cross section throughout, most likely box section. Your main concern will be making the surfaces on which the Y-axis rails mount sufficiently accurate, i.e. parallel. It's much easier if you mount both the rails in the same plane (i.e. on the 'front') since you can then just use epoxy granite if necessary to obtain the required flat surface. Using that orientation does however increase the overhang of Z, but I think that's not a big problem given how strong the gantry will be.

Any discussion of structures failing is hardly relevant, since in a CNC machine we are aiming to obtain a certain level of stiffness, not just aiming to ensure the material does not fail. That is why to the beginner the designs can look over engineered, since the size of material used is comparable to much larger structures. The critical difference is in civil engineering the allowable deflection is substantially greater - nobody cares if a stage truss deflects by a couple of millimetres, but if your gantry deflects by just 0.1mm you could be in trouble.