Excellent point, NU. If a longer lens gives enough resolution for the task, then it has lots of advantages.
You've mentioned ease of illumination.
Accuracy of scale bars and quality of stacking can be others. Shooting from farther away, the longer lens will see less scale change from front to back of the stack. If you're focusing by changing the subject-to-lens distance, then the entrance pupil of the longer lens will move less, in an angular sense, which reduces one source of halo. And if you do go the extra mile to make the optics telecentric by adding an
auxiliary lens near the subject, the longer lens gives more space to do that.
As illustrated by your example, the longer lens will typically have its best resolution at a larger f-number than the shorter lens does. In my Olympus bellows lens series, the 38 mm f/2.8 is slightly best wide open and almost as good at f/4, while the 80 mm f/4 is best at f/5.6, and the 135 mm f/4.5 is best at f/8. That larger best f-number is a lot of what contributes to the lower resolution of the longer lens.
The upside to the larger f-number is that it gives more DOF per slice, which allows a larger focus step and fewer frames in the stack, which makes it quicker to shoot and process.
These are all tradeoffs in the optimization game.
--Rik
Edit: to clarify terminology about aperture size (f-number).
