It works the same as for someone who changes lease, if i’m not mistaken. At least so far (we’re currently waiting on our second car) there’s no difference.
It needs to be “officially confirmed” twice, basically. Once by Motability, which you can check online and i think you’ll get mail, too. The second would be by the dealership, which ties into the “what if it’s pulled” question.
You ordering in a dealership doesn’t actually mean that it’s ordered. The dealership needs to place the order with the factory, then the order is confirmed and it doesn’t matter if the car’s removed from the scheme. The problem some people faced recently was that dealerships were sitting on their orders for one reason or another, didn’t place the factory order immediately, and when the car got removed from the scheme and the dealer then eventually tried to place the order, the system wouldn’t let them which leads to a cancellation from the dealers side. Which can happen months after you (thought you) ordered.
So, walk in, order the car, pay a deposit (usually if you order additional extras), check online in your Motability account the application – once that goes through, check with your dealership if they placed the order. That’s basically it.