When having only 2D GCPs, in order to georeference the model:
1. Create a project: Step 2. Creating a Project.
2. Import and mark the 2D GCPs: How to include GCPs in the project.
3. Run step 1. Initial Processing.
4. On the Menu bar, click Project > GCP/Manual Tie Point Manager...
5. Change the Type of the GCPs from 2D GCP to 3D GCP.
6. Set the Accuracy Vert to a big value, e.g. 5 meters, and click OK.
7. On the Menu bar, click Process > Reoptimize.