I'm a bit confused about the Mods folder in the Editor folder. For me, the Mods folder is just in the main Data directory, not the Editor folder (though, admittedly, I did make the Mods folder there a while back for Scales), and all the data seems to go there fine. Might that be creating issues for me?
Not sure if I understand your question correctly.
There is a specific way how mod files are organized in the editor. Let's say we treat Data folder as a root folder for game data. Then all your files organization will look like something like this:
Data/Editor/Mods/YourMod/Levels -> Some Levels
This folder mostly store terrain geometry and AI grid data
Data/Mods/YourMod/
--> Story
--> Globals
--> Levels
etc.
This folder for osiris files, levels, global objects and such
Data/Public/YourMod/
--> Stats
--> Scripts
etc
This folder for stat files, root templates and such
Data/Mod/YourMod and Data/Public/YourMod folders are created automatically when mod is created, but Editor folder in created only when some level is created. I made tutorial for the case of blank mod, that's why I told to create it manually.