If this attitude from ATOC is not concrete evidence that private companies shouldn't be let anywhere near OUR Railway, I don't know what is. Who do we vote for for nationalisation? Certainly not Mr Leech, put it that way.
I don't see your problem. There has ALWAYS (since BR days) been an option to travel via Manchester,
but at a premium. The ANY PERMITTED ticket was never valid via Manchester under normal circumstances, and you would have had to of purchased the specific VIA MANCHESTER fare.
The removal of the premium VIA MANCHESTER fare seems to be the issue, but if this is reintroduced, it would obviously have to be at a higher level than the Liverpool and Manchester - London fares to reflect the enhanced validity.
Nationalised or not, nobody has ever allowed you to travel Liverpool-London via Manchester except during engineering works, WITHOUT paying for the premium routed VIA MANCHESTER fare. (The fact they forgot to remove the engineering easement isn't surprising, but doesn't mean it should stay forever).
Like I said, the more (and very) reasonable route via Warrington being removed should be the focus!
Ask ATOC/VWC to create a new VIA MANCHESTER fare, I'd say £4-£5 higher than Manchester-London.