Nicholas,
Being aligned with the centerline is only important if one has a very narrow runway. Some operators, and indeed some avaition authorities, encourage aligning off-center in order to make the airplane more visible (particularly at night). An airplane on the centerline can blend in with the centerline lights, and may be more difficult to see for an aircraft approaching to land.
Some pilots prefer to offset a few feet either side of the centerline in order to keep from listening to the bumping sound of ruway centerline lights under the nosewheels.
Aligning with the centerline isn't a problem. One can simply drift back onto it during the takeoff roll, if desired.