Sean,
From my experience, if you're off center a bit, it's not a big deal as LONG AS the engine is still running parallel to the pipe. In other words, as long as the engine is blowing straight down the pipe and not towards one side you'll be ok. Depending of course on how far off center your engine is. An engine that is perfectly centered by crooked will damage a pipe quickly. If you're within probably 3/16" of center but running straight down the pipe you'll probably be ok.
Your mileage may vary...