Know what, I just got done rebuilding my bass (same p'ups BTW) and had a similar problem with my D and G strings -
Mine is a Washburn. Immediately after taking this pic, I moved the p'up over to align properly. However, I had to take my Dremel tool to my pick guard in order for it to fit properly. Which is no big deal since
any pick guard I've ever put on doesn't line up properly, so I'm used to doing this.
As for having an effect on the sound, some will most assuredly say it has an effect. Personally, I didn't notice much difference, if any. But knowing it wasn't lined up properly would have driven me nuts.