There are numerous reasons for this. Clinically, you want to scan the jaw with the implant without the scanbody in place so that you can have access to the contact areas of the adjacent teeth. More importantly, the scanbody can be taller than the adjacent teeth, which would throw off the buccal bite capture when trying to relate the upper jaw to the lower jaw.
When you image the scanbody in the the Medit iScan software, the data is ignored for the occlusion calculation. When you, or a lab design with the scanbody, they also have to “feed the CAD Software” the right information. 3Shape software requires that 3 models be imported in a specific sequence: the jaw, the jaw with the scanbody ALREADY merged, and the opposing. If the designer is a novice, they may struggle with this and reject your case. There are numerous work arounds and easy fixes for this, but a good practice is to image them separately for all the benefits outlined above.