Note that the new NRCoT allow a Penalty Fare to be charged for a ticket invalid due to time restrictions, which was not the case before.
I don't see how anything has changed here. The new wording might be "simpler" but it doesn't change the actual Penalty Fares schemes it is merely attempting to summarise.
The SRA Policy which still governs all Penalty Fares schemes is unequivocal:
Ticket restrictions. Many types of ticket cannot be used at certain times of day, on certain days of the week or on certain trains. These ticket restrictions can be complicated, and even familiar tickets such as cheap day returns can have different restrictions on different routes. If a passenger travels on a train on which their ticket is not valid, it is more likely that the restrictions were not properly explained to them than that they are deliberately trying to avoid paying the right fare. We believe that it is up to the train operators to make sure that each passenger understands the restrictions which apply to the ticket which they are sold. Under rule 7, a passenger may not be charged a penalty fare if he or she has a ticket for the journey which they are making that is not valid on that train only because of a ticket restriction. In these cases, the passenger only needs to pay the excess fare, in line with the National Rail Conditions of Carriage.
And the old wording supporting this is still present, now in 9.4:
If you have an ‘off-peak’ or ‘super off-peak’ Ticket, correctly dated but invalid for the service on which you are travelling; you are using a route for which your Ticket is not valid; or you break your journey when you are not permitted to do so, you will be charged the difference between the fare that you have paid and the lowest price Ticket that is valid for the train you are using.
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Remember, Penalty Fares meant to offer a fast-track resolution in situations where it is reasonable to infer that the passenger is being dishonest and could (in principle) be prosecuted successfully under RORA. (Typically, the passenger ignored both unambiguous signage insisting that he or she pay before travelling and usable ticketing facilities.) Where the facts of a situation can also be explained reasonably in an alternative way that does not demonstrate deliberate evasion, then allowing a Penalty Fare to be issued is inappropriate, and I think that that's what the Rules are trying to cover here and why they have to err on the safe side.
You hold an Advance ticket that clearly states it's only valid on a different train? Safe to assume you know what you are doing and attempting to avoid buying a new one.
You hold an Off-Peak ticket that's invalid because of rarely-simple restrictions? The Penalty Fares system has to give you the benefit of the doubt for the reasons the policy lays out, but that doesn't preclude the direct use of RORA where sufficient evidence of deliberate evasion is present.
