Yes, the 1/2 spline misalignment will cause a small vibration, but probably not enough to cause premature wear of the U-joints. It will only be a driver comfort concern. If you can live with a slightly imperfect arrangement, go for it. If the shop that re-tubed the shaft is willing to correct their mistake, take the mating slip yoke that fits the misaligned spline with you so they can index it properly as it's rewelded.
Jerry
