I have read through this thread over the past few days and have purposely stayed out. There are some reasonable explanations in this thread and others that don't show a real understanding of time & phase..... I will try to provide an accurate and very simple explanation.
Over all time alignment is addressed. All frequencies travel at the same speed, Just because one frequencies wave length is longer, does not mean that the frontal wave of one frequency will reach you at a different time as another.
On speaker design what we align is the portion of each driver where the sound is emitted, which is normally, aligning the front of each voice coil. This allows all drivers sound to reach the ear at the same time. .... drivers can be staggered or sloped.
Phasing.... fairly simple actually.... If it were possible to have a PERFECTLY phased speaker, which does not exist, 2 way, 3 way 4 way does not matter. In each of these speakers, perfect phasing means all speakers cone movement would operate in unison. This really cannot happen, so perfect phase cannot happen. What we normally do is to get phase alignment at the crossover frequency. When each driver is in phase at the crossover frequency, you normally get a quite good sound stage. Each crossover type will cause some sort of phase shift, normally 60 to 180 degrees out of phase. With alot of work, I have seen some drivers as close as 15 degrees of absolute phase with another, but normally achieving near phase alignment at the crossover point works very well. If you think about it in frequency, its fairly easy to understand why you cannot achieve absolute phase alignment. a tweeter may produce 3000 hz and up, well its obvious that the tweeter is moving at 3000 cycles per second, so a woofer moving at 60 cycles, obviously cannot produce sound waves in perfect unison. Each driver does its job and we do the best that we can to produce time and phase alignment. The better that alignment the better soundstage and imaging are produced. If you think about it in the deepest sense, Phase really is time, if drivers are out of phase with each other, frequencies are leaving the drivers at different times, thus effecting time alignment. I hope this all makes sense and helps in some way. Tim