No, do not include the 3D camera. You need to keep the 3D camera in the shot so the Mask layer will move with the camera. The mask layer should be just in front of the projection layer you have that is closest to the camera. You are only pre-composing the 'projection' layers to group them so you can use one track matte for all layers. Without the camera left in the original comp you are essentially replacing the camera created with the camera tracker with the default Active Camera so none of your tracking info is being used.
I wouldn't call this projection mapping. It is more like matte painting because you are painting an element in a shot that wasn't there. Calling it projection mapping confused me for a bit.