the outcome would likely be that train companies stopped doing settlements
The outcome should simply be that train companies settled for the amount they were entitled to receive - no more and no less. Purely to make good their actual loss in each case - no artificially-inflated sums (and I'd argue they can't even include enforcement overheads which should already be covered by the ticket prices).
Alternatively they could impose more Penalty Fares (from which they are allowed to profit) should they feel like taking the trouble to adhere to those regulations...
Is your position is that passengers being charged Anytime fares on board to rectify irregularities is somehow illegal or not in the passenger contract?
I think it's happening due to the "long memory" that many parts of the railway have. It used to be the case in the old Conditions of Carriage, but for unknown reasons, whether deliberate or accidental, those terms are gone now.
I think in a civil case, it's basically the lowest-priced walk-up fare for the journey now, and in a criminal case it's still the best judgement of whatever ticket(s) that particular passenger (or type of passenger) would have used had they not committed the offence.
I accept island's point that most people in this situation aren't going to quibble because of the power dynamics, but that's only more reason why the ORR ought to be looking into what's going on here and making sure everything is happening on a firm legal foundation, and if it finds there have been some inflated settlements, the train companies should have to put them right.