Thank you for letting me know! I'm not an expert at mods but I would love to look into this if you're able.
Essentially, the issue is that although you can research optimization tech productivity in the tech tree, it doesn't get applied to the Krastorio building (called: research server) that produces the science (whereas all other science produced from the research server do correctly receive the productivity bonus from your mod). Muluna changes where optimization science is in the tech tree. That's what I thought might be the issue...
My mod versions are:
Factorio: 2.0.72
Muluna Moon of Nauvis: 2.1.70
Craft Efficiency: 0.2.20
Krastorio 2 Spaced Out: 1.5.13
Were there other details you were wondering about to look into this? Thanks again!