I'm using Krastorio 2, as well as Space Exploration, and it seems to only affect the 'vanilla' items. Everything unique to these mods seems to be unaffected by the speed upgrade.
I tried crafting Krastorio 2 (version 1.3.4)and Space Exploration (version 0.6.85) items, with both loaded together, and, unfortunately, could not replicate the issue. Do you have a full list of mods you are using?
