Eye diagrams can be negatively impacted by wrong ESD protection selection. An extremely high capacitance ESD protection may cause the eye diagram test to fail.
On the other hand requirements like attach / detach requirements (more functional) cannot be impacted by the ESD protection because ESD protection is transparent (high impedance and low capacitance in parallel with datalines) in normal operation.
TD 4.1.2 is related to USB Type-C test for Rp that must not be present for source application when source is OFF. ESD protection will be transparent in this test.
TD 4.12.2 is related to USB Type-C test checking if there is only one upstream port in a hub port device.