Never heard of the 3x3 Godot format before, this project uses the basic(?) Godot tileset system.
The image you included is a blob tileset (47 tiles), but mine is a Wang tileset (16 tiles). You can access the blob tileset (obsolete) at: Hana Caraka - Topdown Tileset\Version 2.0\
Animated tiles in Godot are quite different from static tiles, so I’d recommend checking out their official tutorial or documentation.