NADCAP has a section devoted to compliant pin.  This cross references the IPC requirements.

COMPLIANT PIN (PRESS FIT) CONNECTOR INSTALLATION COMPLIANCE
Is the compliant pin assembly personnel trained for the task being performed and are training records available and up to date?
Is the tool defined in the procedure being used? 
** Are the assemblies inspected for compliant pin insertion compliance in accordance with the requirements? **
** Does the supplier control the press to prevent compressive damage to the assembly and ensure compliance? **
If rework is performed, is it done according to the procedure?  

As you may note from the questions, the criteria center around compliant pin manufacturer guidelines, which typical requires full engagement of the binding feature of the pin.
Protrusion is not a requirement as most backplane boards are thicker than the pin length.  This allowed for/by IPC as it is a pre-established lead length.