Ha! Maybe, but honestly, I would put it down to sample variation or even a slightly different focus position (you are manually focusing, so even a tiny difference could affect the sharpness.)
I did a LOT of research (I mean a LOT) when I got interested in C/Y lenses a few years ago, and the general consensus is that there were no optical changes to the lenses when they went from AE to MM. A few lenses *may* have had some very small tweaks, but the main difference is the aperture blade movement and more mature T* coatings. (Which could contribute to the better performance in your 28/2.8 test!)
If you ever want to treat yourself, pick up a C/Y 100mm f/2 Planar. Probably the "best" lens I have ever owned. (And I've owned many.) Critically sharp from edge to edge even wide open at f/2, with very little CA or fringing (only visible in extreme conditions), and all that Zeiss micro contrast, color and pop. Even the Bokeh is smoother and more pleasing than most "Zeiss" designed lenses. It is arguably the crown jewel of the C/Y line.