I only noticed time alignment issues with present highly modded Klipschorns when in stock form. Originally mid driver and tweeter mounted on same baffle, mid driver sat probably 17" behind tweeter, this due to long exponential horn on mids. My mods replaced stock horn with Volti tractrix and tweeter mounted on separate baffle. I've mounted tweeter baffle essentially in line with mid driver. In stock form Klipschorns and some other Klipsch perceived as bright, certainly true with mine in stock form. Better time alignment has meant better tonal balance, no more of that beaming high and mid high freq., also far superior imaging, sound staging. But then, this was extreme example of poor time alignment.
My Merlin VSM-MM never had perceptual time alignment issues. Having said that, I did run Omega single drivers with 2a3 at one time, coherence was really something special, even compared to Merlins, a two way which have rep as being very coherent.
As for phase, I recall seeing a website some years ago where someone measured and listed cd's recorded in proper and reversed phase, turned out recordings pretty random here, reason for phase switches on many dacs.