In order for Kerbal Addons to be compatible with the Twitch Desktop App, they must follow a standardized structure.
The structure is as follows
├── Addon Root Folder (typically named after the Addon)
│ ├── Addon Contents
│ └── Additional Sub Folders as Needed
├── Other Addon's Root Folders
| └── Their Contents
This Structure will allow Addons to be managed by the Twitch Desktop App successfully and coexist with other Addons. A good example of this layout is the MechJeb Addon which shows the proper structure.