That depends if your using the transmission line as sort of an inifinate baffle with no real ported output, or if your using as one long port as opposed to rear horn loading, the later of the two introduce group delays that have higher delay times than the typical vented enclosure. If I remember right there is an article somewhere on the audiohilics site, that gives a little light to the subject about how little it really means in actual audibility, when I have the time to search for it I will post it, unless somebody else can bring it to light for all of us. I'm not gonna say one type of alignment is better than another, they all produce they're own benefits and deficiency's, and most people would be none the wiser due to how the human ear peceives sound, it is remarkable adaptive. Hence the topics about double blind tests and the statements that the hearing memmory is only about 4 seconds.
This is a subject that we could all argue on for months and never come to a scientific conclusion, because, well, their is no real scientific proof of any of it, acoustics is about as subjective of a science the biochemistry of the brain, and as difficult to disprove as quantum physics.
In my honest opinion, it doesn't really matter if you use two 8's or one 10, if you use the proper alignment coupled with the right midrange if necessary and the appropriate crossover, you will get as close to equal sounding speaker systems as you can get providing all other factors are equal, which in all practicallity, will most likely never be equal.