The premium rate of VED is based on the list price plus options at the time of purchase, so although you paid less than this, at the time of purchase the list price was in excess of £40,000 so unfortunately it qualifies for the premium rate. This avoids dealers being able to offer discounts in order to avoid the premium rate.

The difference with the previous question you're referring to is that at the time of purchase the list price was below £40,000, but the list price had passed this before the order was completed.