The diagram indicates that the upper loop (or loops*) affects the lower loop, but the opposite is not true. Therefore the stability of the upper loop (or loops) is unaffected by activity in the lower loop. Since the lower loop does not affect the upper loop, the input from the upper loop to the lower loop can be regarded as a disturbance input to the lower loop, and analyzed accordingly.
It seems a bit odd to me that the angle tracking loops produce a "reference voltage", and the input to the lower loop is "Solar panel voltage". I would expect the solar panel voltage to be an output from the panel tracking. But it's not my field.
*The upper part of your diagram has two inputs (angles) and two outputs (angles), so it looks like there are two transfer functions, not one, related to the upper part of the diagram. The output angles are inputs to the "Position Irradiance Temperature" block, the output from which is an input to the lower loop.
