On 2023-12-28, a JLCPCB support agent told me that:
- SMT components are assembled according to the 2D picture
- Through hole components are assembled according to the 3D rendering
Therefore, you can ignore it if your through hole part looks slightly misplaced in the 2D rendering. It will always be assembled according to the placement 3D rendering.
Note: While I checked this information with the JLCPCB customer support, I do not take any responsibility beyond what’s required by law, for the correctness of this information. In other words: If your PCBs get mis-assembled, don’t blaim me. If in doubt, check with JLCPCB customer support. It’s not like they make it hard for you.