Their response gave you until 28 Nov. to pay the discount, therefore you should be in full penalty territory now. You might check on their website.
The PCN was served on 3 July,
Therefore, as their letter observes, they have until 3 Jan. to serve a NTO.
If they're still dealing with matters in a chronological order, then perhaps they'd miss the deadline. IMO, let sleeping dogs lie until then, after all it's only 13/14 working days hence.
The NTO would give the registered keeper 28 days in which to make formal reps, plenty of time to measure bays or whatever and compare with regulatory requirements.