Yes phase issues plague the world of a 3 way setup and it's very difficult to get things right,what may work for me may not work for you.I've ran multiple configurations including the one similar to yours in my installs over the years and have found my preference to stand with the current one.
The most phase dependent frequency range lies from 20hz to around 2k,what drivers play these frequencies in a 3 way setup?
ANS: The midbass and the midrange.So when you're getting them close,especially the midrange in the kicks you get physically equal PLDs.
GlassWolf's Pages
What frequencies are important for stage heightThe dimensions of the outer ear can only have an effect upon frequencies above ~2kHz. Which means frequencies below that point can be physically low and still be perceived as high. (That is assuming the 2khz and up region is high or is perceived as high)
The most important point of this post: Our ears do not perceive physical height, they perceive the frequency modifications that our ears make upon sources of different heights.
What does that mean in your car? It means that you have to replicate the characteristics of a high stage.
Second point: Your drivers (even tweeters) do NOT have to be physically high to have stage height
One way to get stage height would be to make sure frequencies above 2khz are physically high. BUT, what about tweets down low, such as doors or kick panels? If you tune your tweeters to replicate the frequency characteristics your ears would have if they were mounted higher, you will perceive just as high a soundstageThat's a BIG point. It means that if your tweeters are low, you can tune them to replicate a frequency response associated with a higher source. A lot of times you reap the benefits of not being directly beside a reflective surface as well.
Now to get the ball rolling and dig into the good stuff 
This part of the tutorial will start to cover general theory into system design.
Plus a part of the reason why I ran midranges in the kicks is that when up there on dash the midrange frequencies create absolute havoc as compared to the higher frequencies the tweeter plays plus one can tune all they want but the physical dimension of having the driver too much "in your face" can't be eliminated.Tuning goes a long way to improve things but a bad speaker location can't be fixed with it.
Lots of people have used the same placement on DIYMA with success and without any issues of height.I personally feel that when you complained about the auto EQ on the 80prs sucking,it wasn't the auto EQ which was at fault.We've had success with it in 3 different builds (frosty,mark x and heisenberg) and yes there has been input after the initial tune but the auto EQ curve used was the pioneer curve.With that being said it is part of the learning curve and I encourage you to try maximum locations until you get to the best one,there's no right and wrong.
p.s another reason why the auto TA and EQ is helpful is the fact that it gets you in the ballpark,let's say you intend to try a new slope or a new crossover point you can easily try it out within a matter of minutes rather than spending lots of time tuning in for a new crossover point or a slope.I repeat the user input is still required to get things right just like any other machine.
Alpine - - SPX-Z18T
Kindly download the user manual for these components here,this is a freakishly expensive set abroad and why? I'd say the engineers did a fine job especially in the crossover department and you'd have to hear it full passive to believe it.Never have I seen such a design where they gave out options to choose settings passively for multiple types of installs.So predetermined close to flat response is quite achievable if the install is pulled off right.
