It seems if you are using a texture atlas and Texture.fromTexture, there's no way to generate mipmaps?
Ah, yes, that's true. Mipmaps can only be used on the low-level master texture — subTextures inherit them from their base texture, but they can't have them on their own. That's probably the reason why you didn't see any textures when using your classes.
So you need to decide on mipmaps for each atlas texture. The AssetManager can be used to enable mipmapping on specific textures:
assets.textureOptions.mipMapping = true;
assets.textureOptions.mipMapping = false;
Ah, and one more thing: you might want to extend the one-pixel border. E.g. if you want to scale the object down to 25% (1/4th), make that border 4 pixels wide. For 1/8th, 8 pixels, etc.