Notice how the frames march closer as focus gets closer as though the lens zoomed.
I actually think it did zoom but I'm clueless how and/or why.
As you change the focus in a macro lens, the magnification changes.
You can see it if you turn off AF, prefocus at the "further" range, move in manually until the object is in focus, then repeat closer in. The object will become larger in the viewfinder.
The magnification ratios are different, and that is printed on the focus scale (1.5:1, 1.2:1,1:1- or however they are laid out).
I believe the technical term is focus breathing- could be wrong.
The only way to keep the magnification the same and change the focus point is to preset your focus, turn off AF and move the camera in/out to focus the desired point. Best way to move the camera is with a set of gear driven (manual or motorized) focus rails. Any precision or repeatability without a gear driven system is damn near impossible.
I have a set of rails and have messed with an MPE-65, and I can see the focus change as the setup is moved on the rails. It doesn't take much movement. Apparent magnification (object size) does not change. Moving the tripod in and out proved to be useless.
I found it quite interesting, but it is very time consuming.
I suspect that the apps using focus stacking vs rail movement are stretching/shrinking the sharp parts of the image to blend it together for the final result with assumed quality loss (small image is expanded and large final image is shrunk). I would assume it picks somewhere in the middle as a starting point for final image size/scale.
There is a lot of skill in a good focus stacked image.