I've thought about this a lot. ;D
One should remember that manifold mounting places another driver cone opposite each driver cone.
The opposing panel area is (usually) relatively small in comparison with the area of the opposed driver cones.
The driver cones are not flat. (unlike a panel) Are at least partially acoustically transparent but are also usually moving linearly towards and away from the opposing cone. If only a little. Though the change in their spacing is effectively doubled. Which means that distance-related boundary effects between cones are constantly changing.
Which means that any reflection effects between these opposing, irregular surfaces are very unlikely to peak at certain frequencies. i.e. No standing waves. Which reduces the likelihood of any boxy colouration.
Further, the frequency of inter-boundary effects is likely to be well outside the pass band of the IB.
If, like myself, you find you cannot sleep at night for worrying about these things
then just make the opposing walls of the manifold non-parallel. Thereby removing all potential criticism of the manifold as an unwanted box in your IB system.
In fact, provided that you have the woodworking skills, or a complete lack of them, there is really no need for any two surfaces of the manifold to be parallel.
Just be sure to report back on your extended A/B/X comparisons with a standard square (box) manifold. So that we too may be "improved".
Don't think I'm making fun of you. I greatly admire those who seek improvements to the standard IB prescription. Most of the likely improvements (in my own limited experience) come from stiffening the box itself so that the driver baskets remain totally unmoving relative to each other and to their surroundings.
Those seeking the best SQ could well look at concrete or a similarly stiff, massive and rigid medium (like bricks or slabs) for either a manifold or an array baffle wall.
Those who prefer more normal, laminated boxes should consider stacking smaller, 2-opposed driver manifolds. Rather than aiming for one huge, but flexible, multi-driver, vertical manifold. (like mine)
The thicker tops and bottoms of the smaller manifolds will stiffen the assembly better than adding shelves as an afterthought. It will also make the installation of an IB, containing a larger number of drivers, much easier. At least, compared with manhandling a single, huge and heavy box.