There are two aspects to this. Firstly the technicalities about whether or not it was issued in accordance with the regulations, indeed ignored in the response. Secondly, the scope of what the appeals process was meant to be doing (and that's really for Transport Focus to sort out with the Appeals Panels).
On the second point, the implementation has become too narrow, in that the various responses we see tend to focus merely on "Was the inspector entitled to issue the penalty?" but that's only the first part of the question and wouldn't normally be the main thing people deciding appeals need to focus on. Often there's no dispute - yes of course the inspector was entitled to issue it - but that has no bearing on whether or not an appeal should be upheld. In fact, those inspectors who have some doubts about the passenger's explanation so issue the penalty and then advise the passenger to appeal are the ones understanding the system as it was intended to work, as the appeals body can make the extra checks that the inspector can't, to satisfy itself there was no dishonesty. The appeals system then lets everyone down by not striking the balance parliament intended. Recall that someone who loses their ticket is, if everything checks out, unlikely to be expected to have to pay the penalty. I think a dead battery where the ticket already got scanned at the gate is an even more clear-cut example of a "compelling reason" why it would be wrong to impose a penalty for intentional fare avoidance (which is what a Penalty Fare still is, notwithstanding the efforts of some operators to broaden its scope).