I never said it did! But you do need to have accepted it before the delay became known to you regardless of when in the journey that was.
I just wanted to preempt that potential argument

but yes, any PFs issued at the destination would probably be ineligible for compensation. In fairness the NRCoT don't explicitly state this exclusion, it is only contained in some Passenger Charters.
Has anyone here ever objected to the many cases where passenegrs win on appeal and are instructed to pay only the fare due to dispose of their obligation to pay for their journey? It seems quite clear to me there are two elements to a penalty fare. The penalty, and the fare (which is not a penalty at all and should reflect the appropriate cheapest fare for the journey being made).
That happens simply because it's what the Regulations require. Regulation 16(11A) refers:
(11A) If an appeal is against a penalty fare calculated in accordance with regulation 9(1A) or (4A) [i.e. an English PF], where the relevant Appeal Panel—
(a) notifies the operator that an appeal has been allowed; or
(b) fails to adhere to the time period specified in paragraph 6 of Schedule 2, the appellant is not liable to pay the penalty fare in question and is only liable to pay the full single fare applicable for their journey.
It replaces the liability to pay the PF with a liability to pay the full single fare. In respect of Welsh PFs a successful PF leaves the appellant with no liability whatsoever; this was the case for all PFs before the increase to £100 for English PFs.
It's not a question of objecting or otherwise but simply looking at what the PF Regulations and the NRCoT say and then working out how the two interact.
The key thing about a Penalty Fare is that the passenger is in the wrong and has breached the contract, and therefore does not have one at all until they are Penalty Fared. That is unlike a passenger who acts in accordance with the contract by boarding legitimately and as invited without a ticket with a promise to pay later where there are no facilities to do so before boarding.
PFs have been issued in situations where the NRCoT state that the passenger is merely liable to pay an excess - for example when breaking a journey where not permitted (e.g. on an Advance), or using an Off-Peak ticket at a restricted time.
Whilst clearly the NRCoT don't intend a PF to be the way such situations are dealt with, it's difficult to appeal such PFs on the grounds that the ticket was valid (because it wasn't, in the way it was used). It's also tricky to say that the NRCoT section about excesses amounts to permission to board a train without a valid ticket.
I say this to make the point that not every PF is a result of a fundamental breach of contract. And even if there is a breach of contract - so what? It doesn't mean that all the other provisions of the contract stop applying. If the industry wants Delay Repay to be excluded then it needs to explicitly say so. It already does so for the 'published timetable' nonsense; it's perfectly capable of adding more exclusions.