Does the NFM count as part of the contract in terms of looking up restrictions, or is there another source I should be referring to in terms of being contractually enforceable?
If it is made available or accessible or if it is at least possible for both parties to refer to the restrictions, then it may be considered as a source of binding and applicable conditions. Yes.
But I am not persuaded that the Manual IS available, accessible or possible to refer to.
I have not attempted to find another source of the resrictions - perhaps they are available while selecting tickets from on-line booking engines? (and perhaps 'the error' is perpetrated there too?).
As far as I can see if that restriction is part of the contract, FGW would have a pretty hard time stopping me from travelling in the evening as all the outward restriction says is after the morning peak.
As I said above, if it is going to be apparent what was intended by the poorly written restriction, then I would expect officers/staff to apply it - as intended. And you would be unreasonable to expect otherwise. You should be ready to accept an UPFN.
The appropriate time to dispute would be either when buying the ticket or when challenging the payment of a UPFN after travel. Depending on factors on the day, you may find that the staff enforcing 'the error' when you travel do have the time, interest and inclination to read a print-out from the Manual and agree with you. I would call that good fortune.