It doesn't make a difference to you if its pre-registered, it just means that the company you bought it through will be down as the first registered keeper on the V5. To be honest, who cares about that?

I've bought mine pre-registered too. Its a factory order also (as are nearly all ST orders nows), its just the company is buying the car first, then I'm buying it from them. It makes sense when you're saving so much off list price (mine works out at a £2,600 saving), you're unlikely to find a deal anywhere near as good on a car where you'll be first keeper. I'll never buy a car from a franchised dealer again...