This applies to aligning newly recorded tracks with previously recorded tracks, and properly compensating via ADC for hardware inserts. The H/W Insert Delay Compensation setting in the I/O setup is not designed for this.
Pro Tools should be able to properly compensate for the A/D - D/A conversion delay of any hardware, not just Digi hardware. Currently, recording pass compensation is only correctly applied to inputs from Digi converters. Using external converters via digital inputs or Apogee interfaces with X-HD cards entails additional delay that Pro Tools cannot take into account.
At the very least, there should be a delay values tab in the hardware setup that allows us to enter the actual delay value of every input/output. Digidesign should also publish a look-up table with the conversion delay values of all known converters, and provide instructions to their users on how to discover the values for themselves.