Steps to reproduce:
1. Download and open the project "Issue-Built-In-SG-GPU-Instancing.zip"
2. Open Assets/SampleScene.unity
3. Notice that the Shader for the Red Sphere is misaligned with the GameObject
4. Click on the GameObject "Sphere (Red - Shader Graph Material)"
5. In the Inspector, Toggle "Enable GPU Instancing" on and off

Expected result: The Shader is aligned with the Sphere GameObject when Enable GPU Instancing is on.
Actual result: The Shader is misaligned with the Sphere GameObject when Enable GPU Instancing is on.

Reproducible with: 12.0.0 (2021.2.0b4)
Could not test with: 7.6.0 (2019.4.29f1), 10.5.1 (2020.3.14f1), 11.0.0 (2021.1.15f1) (No Target for Built-in Render Pipeline)

Note:
The Enable GPU Instancing option is unavailable in some versions, but the issue is still present