I think the phase lead has more to do with the charging of the capacitors because of the AC nature of an audio signal. Basically, it comes down to math that for this thread is over the top. While I won't say it physically advances in time, the phase shift in the positive direction ( which indicates a phase shift that is ahead in time ) does preclude the signal. Looking at the webpage I directed, it prescribes that the input starts at +45* ahead of the input and then of course shifts to the nominal phase shortly thereafter. The lower portion of the passband does not shift back to zero however. In either case, it is a phenomenon and a consideration.
When we use Smaart and other such tools to align the phase slopes, the phase shift of the subs relative to the mains is a measurement of the acoustic average and not so much the electrical anomalies that math prescribes. The averaging, weighting and sample frequency of the measurement is surely much lower in resolution than the electrical actuality, not that we could " see it " in the air anyway. In short, we simply couldn't see or hear that phase lead anyway. We align the impulse/phase slopes to the best we can and it is close enough at the areas that count to work.
Many years have gone by where subs and mains were grossly misaligned and the people have been happy enough if not enthralled by the quality of the sound. Be it by total accident or simply that we can't really tell in a blind situation the basic way that nearly 100% of new " sound guys " have been doing it since the beginning of time has worked well enough for most. The cream rises to the top and those with a greater understanding tend to get better and more consistent results with less work and effort required. Knowing is half the battle while implementing and applying that knowledge is the other half.