As far as the people who send out the NIPs are concerned, you have only two courses of action open to you. You can accept the fixed penalty or you can go to court. Any letter you send to them will be taken as an indication that you've chosen the latter option. So you'll still end up with 3 points on your licence but you'll almost certainly have a bigger fine to pay, plus a £15 'victim surcharge', plus costs.
You're expected to read every road sign you pass. Even if the road had a 50mph limit on it when you travelled one way, but the council had put up 40mph signs when you came back a few minutes later, you'd still have no excuse for exceeding the new limit.
Chris