Very interesting article - thanks for putting it together.
One other thing I've noticed with the Helicon software for a shot which needs to give a wide range of focus is that I can use whatever f/stop is a len's best and worry less about what f/stop will give me the DOF needed.
In the article the Canon 90-TSE was used at f/11. I don't know if f/8 or f/5.6 on this lens is sharper, but if one of them were you can use it, take the set of shots and still get the required DOF.
It seems a little odd doing a landscape at f/4 or f/5.6 (the two apertures which are sharpest in my testing on my CZ 21), but it gives the Helicon the best images to start with.