Question:

Do Viewable Renditions contain Overlays when they are extracted using Vault Loader, Bulk API, or Cart?

Answer:

No, Viewable Renditions do not have Overlays applied when they are extracted using Vault Loader, Bulk API, or Cart. There is no way to configure this currently. This is working as designed.

Related Documentation:

Vault Loader Documentation: Vault Loader: Extracting Metadata & Files