Ignore the alignment, all that matters is the result. Alignments are a relic of the slide rule era, when calcs were so difficult to perform that a few 'alignments' were arrived at to simplify the design process. With software you can arrive at literally thousands of different alignments, which makes choosing from a mere half dozen rather moot. WinISD defaults to whichever of the traditional alignments give the flattest response, but that's only a starting point to tweak from.
On the topic of WinISD, ditch the Beta, it's far too simplistic and only gives a rudimentary result. Alpha Pro is the only way to go. As for transient response, that's only a concern in the midrange, it's of no consequence with a sub. And there's no such thing as tight bass response either, that's a midbass/lower midrange issue, though a poor sub design can result in excess midbass.