The 'procedurally unlawful' thing is weird. Clearly this was discrimination on the grounds of belief.
It's possible for something to be procedurally unlawful, e.g. the difference between unfair dismissal and wrongful dismissal - if you're shit at your job it might be fair to dismiss you but if your employer doesn't follow correct procedure you can still claim wrongful dismissal.
Possibly in this case Nottingham have first accepted that they didn't follow their own procedure, and if they had done so this error would not have been made, and here's a remedy so no point arguing further. And JB has accepted that because here is a remedy. That's fair enough, it would have been very costly for both sides to go to court and judges get pissed off if people escalate to court when a reasonable settlement is already offered.
I think she could have held out for some compensation on top of costs though.