Although both Auto-Align and Pi strive to optimize phase correlation, each one solves a different phase related issues using very different techniques.

Auto-Align was designed to fix the Comb-filter effect caused by multi-mic recording of a single source, where the mics are placed at different distance from the sound source. When summed in a mix, the difference in time of arrival to each mic causes a phase shift that varies throughout the frequency range and cannot be fixed using a phase rotator. Auto-Align automatically detects the distance and the delay between the mics and compensates for it sample accurately.

Pi, is a multi-channel-aware dynamic phase rotator. It analyzes the tracks in your mix in real time and constantly rotates their phase to improve phase correlation. Pi minimizes cancellations of overlapping frequencies when they interact with each-other. Auto-Align is more effective for multi-microphone/ DI recordings, and Pi is suitable for general phase optimization of your mix.