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Per our discussion on the discord;

When meg generates an atlases/blocks.json file with automatic atlas directives, it ignores any textures inside the the minecraft namespace. It turns out that many bbmodel files online use the minecraft namespace as their own, and these files would need to be read into the atlas whether or not they're generated automatically by meg.

As an example, the MCPets patreon welcome gift includes a cat that plays with a ball of yarn. The yarn itself is a bbmodel file with the following texture block:

    "textures": [
        {
            "path": "C:\\<clipped for clarity>\\Premade Resource Pack\\resource pack\\assets\\minecraft\\textures\\nocsy\\toffy_yarn.png",
            "name": "toffy_yarn.png",
            "folder": "nocsy",
            "namespace": "minecraft",
            "id": "2",
            "particle": false,
            "render_mode": "default",
            "visible": true,
            "mode": "bitmap",
            "saved": true,
            "uuid": "328e8016-b785-b0a7-0f07-9ea5886f73d7",
            "relative_path": "../../../Premade Resource Pack/resource pack/assets/minecraft/textures/nocsy/toffy_yarn.png",
            "source": "data:image/png;base64,<removed for clarity>"
        }
    ]

As it is right now, the texture files in this "minecraft/textures/nocsy" subdirectory get ignored.

The solution is to add a source to the generated atlas/blocks.json file that includes this directory.