I dug into this. There's two fixes that needs to be done.
First, Krastorio2 needs to be added as an optional dependency.
Second, the last commit about recycling support is what broke this in the first place. Renaming data-updates.lua to data.lua means the prototypes are copied before K2 updates the entities. This change also breaks for any other mods that updates the entities in the same way. Unfortunately, this seems to be a chicken or the egg problem.
I'm not really a modder, so I don't know how to best solve this issue.