I am using Tiled for a Phaser 3 game and Phaser can only handle maps that have the tilesets embedded. I enabled ‘Embed Tileset’ and wondered why no tiles were exported in the JSON. I then assigned a property to a tile and this tile was exported, but only this one and no others.
If there is no data about a specific tile to be stored, then indeed it will be left out entirely. All tiles implicitly exist based on the size of the tileset image and the tileset parameters like tile size, margin and spacing.