He will have dodged weekly (or longer) seasons, so that is the calculation they need to do - with a fine on top. That current calculation is based on the daily dodge, which of course he is unlikely to have purchased in paying his way.
The prosecution's view is that an offence is committed each time and that the cost of a ticket each day is the loss to the
TOC▸ . That seems reasonable to me. The fact is he chose not to purchase a season ticket offering a discount over the daily rate, so on each day he travelled the TOC's loss was the difference between the fare paid and the full fare payable.
He was ordered to pay back the lower ^6000 amount (ie the cost of weekly seasons) because the Judge held that that was most likely the real loss to the railway. That to me seems perfectly reasonable. The order to pay compensation is not intended to be punishment (that is what his sentence addressed. The ^6000 was not a fine but an order for compensation) but to put the parties back on the footing that they would have been on had the offences not been committed.