Your food shots have given me an apetite:D
Bear in mind that when you refocus with the lens, you will get small changes in perspective & magnification- the distance between the front element and your subject is changing. This could be important when you are focusing so closely. The software is probably correcting for that as well as doing the simpler image combination. Current HDR software will even compensate for small amounts of movement
As Wayne wrote, stacks have to deal with such problems anyway. Refocussing will change magnification (creating a strange distortion), and when the lens to subject changes too (very probable), perspective will as well.
So the stacking software will have to deal with this.
It however is not hard to do: just find, for each point in the image, the image in the stack in which that point is 'sharpest' (by comparing contrast to neighbouring points), and put that in the combined image. Move on to the next point, etc.
Completely ignoring distortion and such issues will produce surprisingly good results.
I think the digital aspect of this discussion is seriously misplaced. The easiest way to gain DOF is to use a longer focal length lens although this introduces a size of eqipment problem. At 1:1 a 420 mm lens at f32 gives a DOF of about an inch (COC .1 mm). In the next couple of weeks, I will do some tests at higher magnifications and smaller aperatures and post them in this thread.
That fickle thing called DOF...
If it were easy to have sufficient DOF, we would not all be chasing after it all the time.
At the same magnification and f/stop, DOF is the same too, no matter how long (or short) the lens.
You could permit larger CoC's in your equation, but that doesn't change actual DOF.
Backing away, and enlarging more will also not increase DOF per sť. It will change how parts of the image look relative to another (i.e. show less difference in sharpness). But at the price of absolute sharpness.
I.e. the gain in DOF is not achieved by getting more sharp, but by reducing the sharpness of the sharp bit so that the difference with the less sharp bit is less obvious.
As the example shows, it works. But it also does not increase DOF.
If analog only, the only real way to increase DOF is the slit light method: move the subject through a very shallow 'plane' of light, positioned where the plane of focus is, exposing only the bit in focus.
The hybrid way, stacking, works, and is much easier.
Perhaps we analog photographers should not always want to be 100% pure? ;)
The hybrid way belongs in a different forum.
The thing that changes with focal length is the rate at which focus changes, i.e. the amount of blur outside the DOF-zone.
But at the same magnification and f-stop, DOF itself is the same, no matter what focal length.
People keep using formulae derived from hyperfocal distance formulae.
In which the focal length figures twice (as F(ocal length) and as M(agnification), though noone can explain why.
They may work for hyperfocal distance calculations, i.e. when DOF is infinite. I don't know. But not for DOF
Every bit of 'proof' offered for the assumption that DOF is different when focal length changes, yet scale remains the same makes use of those same old formulae.
None (not a single one) of the proofs offered on the site linked to holds any water.