The other alternative will be the construction of the oft suggested high speed line between Liverpool and Manchester which would reduce the Chat Moss to a secondary and freight route..
I'd go along with that idea as is the most direct route between the two cities but it is obviously not the quickest south and Lime Street would be unable to handle captive stock. To save going off thread this is best discussed in the HS2 to Merseyside thread.
To be honest I think political considerations will lead to Merseyrail becoming increasingly a closed system - I am really surprised that it survived privatisation as part of the network rather than being hived off at that time as an equivalent to the London Underground...
I'm not so sure, whilst the Liverpool Greater Authority will take over strategic planning of transport from Merseytravel in a slightly enlarged area, it will not include Lancashire, Cheshire, North Wales and of course Greater Manchester, who are all likely to have different agenda.
And those projections for freight traffic to the Port of Liverpool are dangerous since all the projections for the container ports of Britain come out as contradictory - they can't all grow at the rates they claim they will.
Longer freight loops on the Chat Moss and conversion of the freight to electric traction will also allow far heavier trains that will partially ameliorate the problem.
The southern ports of Felixstowe,and Southampton are both chasing the same trades, mainly the Europe Asia and Far East Trades which will continue to grow as all the major shipping lines have vessels of 18000 teu coming on stream over the next few years. At the moment there is over capacity so the lines are dropping sailings at certain times of the year to prevent the rates dropping, but nevertheless the ships in service are still sailing at something like 85% full or more. The reason for the contradictions is that when London Gateway comes completely on stream in perhaps eighteen months time, it too will be targeting the same trades, with Felixstowe likely to be the main target, as the owners of Southampton also own London Gateway. In the meantime the Port of Liverpool riverside terminal Liverpool2 will commence operations towards the end of 2015. This will partly reduce the throughput through the southern ports for containers destined for and shipped from the north of England, depending on the carriers and trade the facility attracts. Felixstowe and London Gateway do not handle bulk traffic, whilst Southampton only handles a small amount of bulk whereas the opening of Liverpool2 will allow the Port of Liverpool to handle more bulk traffic as some of the landside port facilities are switched around, whilst the reduction of containerships negotiating the Gladstone Lock will allow more panamax bulk ships to enter the enclosed lock system. Aside from Liverpool2, the port is developing it's facilities for handling steel and scrap, as well as looking to develop facilities for biomass all of which are seen as growth areas all potential areas of growth for rail transport.
Also as dual voltage stock is apparently no hardship these days (implied by your insistance on it for every job) then why not simply electrify the CLC line with third rail and expect the other services over it to operate with dual voltage trains?
I would think that any Merseyrail extension would see it become the dominant service provider on the route.
My only reason for suggesting Merseyrail order dual voltage stock is that the conversion of the network could then be completed as and when separate extensions are added and/or infrastructure becomes due for replacement. I'm not sure other operators such as TPE and EM would go along with the prospect of having to operate a sub-fleet of dual voltage stock to serve the greater Liverpool area, nor would it help with converting freight movements from diesel to electric traction, even given the limits that are involved.