If the model of the Sun includes only the layers of the Sun’s atmosphere that are typically visible from Earth, it most likely includes the photosphere, chromosphere, and corona. However, the layer that is commonly missing from such a model is the convective zone, which is not an atmospheric layer but rather a layer of the Sun's interior. The convective zone lies below the photosphere and is essential for the solar processes, but it is not part of the solar atmosphere that can be observed directly from Earth under normal circumstances.
If you meant to ask about just the atmospheric layers, then it could be argued that the very innermost part of the atmosphere known as the transition region—the layer between the chromosphere and the corona—might also be considered "missing," as it is not always highlighted in models focusing on more prominent atmospheric layers. However, the more common omission pertains to the convective zone as it is not part of the atmosphere.
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