I've had problems with alignment on two or three different lathes over the past 2 years, and had a number of people tell me "it doesn't really matter" when you're turning. Uh, yes it does. Always thought it did -- solved the problems -- and had my suspicions confirmed when two different, very experienced, demonstrators came to our Club and part way through commented about the Nova DVR demo lathe not being lined up. They both took the time, right then and there, to adjust them before continuing their demos. Same thing when Stuart Batty demo'd in the area last year on a Powermatic. Vibration in the piece is noticeable when ends are misaligned, whether you're turning bowls or spindles.
The second lathe that developed this problem had developed a twist from not being on level footing. Re-leveled, and it relaxed and re-aligned.
What I do now when working on a new lathe is to put a double-ended Morse taper in the headstock, and a long-pointed live center in the tailstock, and extend the spindle to its near-maximum projection. That gives me as much span as can be mustered cheaply. There is a tiny pimple on the ends of those doulbe-morse-taper things, perfect to eye for alignment.
I would not keep a new lathe that definitely couldn't be aligned properly (when perfectly level, etc.). The Old Blue Jet Lathe (1236) doesn't line up, but the tailstock is low, so that's shimmable. Still not perfect, but works for bowls and short spindle work.