Your Simple Shape Shader is appearing as a child of the Fractal Terrain 01, so it's most likely being used as a Mask. This just means that the Simple Shape is being used to control the area of effect of the Fractal Terrain; it is masking the effect of the Fractal Terrain's displacement. Masks are interpreted as black and white, where white is "full effect" and black is "no effect" for the shader being masked. In this case the Fractal Terrain shader's effect is to create displacement (mountains), so with a Mask, where the shader that is going into the Mask input is White you will have mountains and where it is Black you will have no mountains (flat, back to the default, undisplaced planet sphere). In the default scene however it's actually setup with the mask *inverted* (this is a checkbox in the Fractal Terrain's Mask settings at the bottom of its properties), and as a result where the Simple Shape is white (within the 5-sided, 10,000 meters-per-side area) will be *no* displacement (no mountains) from the Fractal Terrain shader, and where there is black from the Simple Shape shader (outside of the shape it defined) will be mountains.
Thus this is the long way around of describing that the flat area you're seeing is not the Simple Shape Shader *making* flat, rather it is the Simple Shape Shader *preventing* the Fractal Terrain shader from making mountains in that area, and thus you are seeing the flat surface of the default planet. *That* is why it is not being raised intuitively, because that flat surface is not being directly caused by the Simple Shape Shader's displacement, but rather because of its use as a mask. It is the *absence* of displacement rather than a subsequent *flattening* of a previously displaced area.
Also to be clear, the height and displacement amplitude of *any* shader have no effect when it is used as a mask because masks only interpret color, the Mask input ignores displacement.
So, long story short, if you want to displace an area controlled by a Simple Shape Shader and use its height or displacement amplitude to control terrain height, don't use it as a Mask for another shader. If you use the Add Terrain button and add another Simple Shape Shader and enable displacement, you should be able to get the effect you want, more or less. However be aware that it will not be inherently flat or smooth! It is applying displacement *on top of* the existing terrain shape created by the shaders above it. Displacement, from any shader, does not inherently create flattening.
To really get the effect of a flat area *within mountains* that you can control with the height of the Simple Shape Shader, I think you'd want to *copy* the Simple Shape Shader you already have, and add it to the node network in-between the Fractal Terrain and Fractal Warp Shader, then enable Displacement. The reason I say copy is so that both Simple Shape Shaders will have the same size and edge settings. The end result should be that you displace (raise or lower) the flat area that has been previously created by the other Simple Shape Shader that is being used as a mask.
OK, I hope that's helpful.
- Oshyan