Penalise in what way? Condition 6 is quite clear about requiring a Permit to Travel (which I think you could reasonably interpret as to include a 'Promise to Pay') if you board at a Penalty Fare station and Condition 10 sets out the penalties that can apply in that case.
Is this an suggestion that TPE are misusing a Promise to Pay (which appears to be for a specific subset of the potential reasons for being unable to purchase a ticket at the origin, and not for all potential reasons) in lieu of the bona-fide Permit to Travel coupons mandated in the legislation, I wonder?
Condition 10 states that an SDS can be charged, or that they can be reported for prosecution. I'm not sure legislation would really come into charging an SDS or other Anytime ticket, that is a matter of contract between the TOC and the passenger, surely? I don't think this particular question regarding being charged a higher price is up for much debate.
Under the NRCoT the full fare can be charged if the customer was able to buy the fare, using their chosen payment method, and simply decided not to. A promise to pay doesn't come into that equation.
Likewise, if the passenger is demonstrating intent to avoid the fare they can be reported for prosecution. Again a Promise to pay is not relevant there.
But I am talking specifically about Penalty Fares and the legislation applying to the issuing of PFs
The prosecution question is a more interesting one. Are you asking whether you think a TOC could get away with prosecuting someone who boarded without a Promise to Pay but did attempt to pay as soon as the Guard came round or at their first opportunity? I think this is an interesting question and I'm not really sure of the answer. Surely it would come down to the same criteria as any prosecution? Do you think a court would entertain that intent to evade under the Regulation of Railways Act could be proven by the lack of a Promise to Pay?
If the customer is paying by cash, there is no opportunity to buy before boarding. There is no requirement in the NRCoT or the law to obtain a promise to pay when paying by cash. This is a suggestion that Northern have made, and now TPE are making that suggestion. But it holds no legal weight and isn't part of the actual Conditions of Travel.