Trust me, I've told Kevin about it too :') He referred me here for your help.

I've done all I could think of, and I indeed too figure it's some sort of engine/game bug. Like, editing an inherited map adds a level of the same name to your mod files etc etc, and I am guessing the journal does something similar. WHICH REMINDS ME:

Can you try this, Tinkerer?

Make a new project, open story editor, copy an existing goal to your mod, then delete it. From my testing, it doesn't revert the Origins goal to default. It actually deletes it entirely. So you'd have to remove the file in the mod folder, deleting it in editor deletes the entire thing completely.