The slice that is in focus will always have the same magnification, so there will be some distortion when stacking. In Helicon Focus that will show as a really weird border around the resulting image. There is some tolerance for that, both Helicon and Zerene can do adjustments to align the pictures, I don't know if they will do single digit percentage resizes or not.
A similar issue exists when keeping the distance the same and changing focus (on a non-fixed focus lens!), all macro lenses that I have used will show heavy focus breathing around MFD, so that may result in an even bigger perspective change than the focus rail.
My focus rail arrived last week, still getting up to speed on 'best practices'. An M6II+MP-E+MR14 is very hit and miss currently, I think I need to practice on a less complex subject. The damselfly exuvia have a lot of overlapping sections that are hard to stack.
This was done handheld using the built-in focus bracketing on the R5II+RF100+EL5, you can see the 'halos' around the legs with the concrete background and around the white cords. I think this is an area where generative 'AI' could be a big help: generating the missing parts and/or removing the bokeh 'haze'. Or learn how to use Photoshop masking and blending
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