This is not "playing with Lego" it's serious scientific research! (Pause for laughter...)
If nothing else, it is answering my questions about how the Stacking software handles differing image sizes.
As requested, I've compiled a couple of Start and Finish images for each technique so that you can judge the relative change in image size.
I still think the software (Affinity in this case) does a remarkable job in accommodating the changes in image size.
However, my thoughts on this are - It may be oversimplifying things just to have the first and last images from the stack, since the software may deal with the differences in different ways.
The other thing is that, with either method, the change in size is going to be different at different subject distances.
In the examples I posted, the working distance between the lens and the subject is relatively large - around 220mm with the 60mm lens that I was using (over 300 mm if you measure to the focal plane.) See test setup pic at the end.
Obviously the greater the working distance, the less apparent the change in magnification will be, with either method although the "focus adjust" will always produce less of a change than the "move the camera" method.
I don't usually shoot with m4/3, I prefer full frame, so I may have a go at some more tests using a different camera and lens to see how they compare.
I notice a good crop of dandelions on my lawn (first signs of spring?) so if I allow some of these to develop seed heads, thay are often a good macro subject, so I may experiment with one of those.
Samples, (I've done my best to show the change by ghosting the difference between the two.)
It's quite apparent that the Focus rack method produces a much larger change in relative image size at this working distance.
First and last images - Vary Focus method:
First and last images - Manual focus rack
Test setup to show working distance.