The core of the issue is the breakdown of the harmonic relationship, and the root cause lies in the inherent physical differences between the speakers.
A subwoofer is designed to move a lot of air for a very narrow bandwidth—often just two octaves. This demanding task, combined with the steep low-pass filter required to confine it, results in a significant inherent processing delay (group delay). In contrast, a satellite speaker, handling a much wider bandwidth of over seven octaves, is a far more agile system with much lower latency.
This timing discrepancy is critical. The higher harmonics (2nd, 3rd, 4th) from the fast satellites arrive at our ears first. Our brain initially attributes the entire sound to them. The fundamental frequency from the delayed subwoofer then arrives later, disconnected from its harmonics.
Because this low-frequency fundamental arrives as a separate, late event without its harmonic context, our ears can localise it to the subwoofer's position. The brain fails to fuse it with the sound from the satellites.
Therefore, the delay from the subwoofer isn't just a minor offset; it's a fundamental timing error that breaks the perceptual link between a note's foundation and its character, allowing the subwoofer to be localised. Time-alignment is essential to compensate for this and re-unite the fundamental with its harmonics.