Ahhh.... I was imagining the Breezer Venturi, or similar bikes.

Still, it sounds rather cosmetic. I am surprised though. The tubes should be metered, so they should line up fairly well during assembly. If the bike was new, I might be more insistent that they "got it right" as it could point to a manufacturing process error (they may not care anyway).

One has a few points on the frame. Head Tube, Seat Tube, (Seat Post, Bottom Bracket), and rear triangle. If all the main components are aligned, then a slight misalignment of one of the tubes connecting them together shouldn't make a big difference.

I'd probably eye-ball whether the stem and fork seemed to align with the seat tube, seat post, and rear wheel. If everything seemed aligned, then just ignore it.