I don't know why it wants to disable so many mods, but I have figured out that the conflict seems to be specifically between this mod and Krastorio 2. This mod's latest update changed the Pump in some way (assumedly the collision mask) and it's caused the Steel Pump to no longer be a valid upgrade/replacement structure.
Re-enabling everything on that list except for either Cargo Ships, OR Krastorio 2, works. Unfortunately until a fix is made you gotta give up one or the other ^^; (or wait, of course. But if you don't have any Cargo Ships stuff built yet you can disable it without losing much aside from any research investments you've put in).