A major layout change you propose there. I think if AC conversion goes ahead NR have to bite the bullet and accept that there will be an area of dual electrification through Basingstoke station and its approaches. All the state of the art mitigations need to be applied to limit and protect against the stray current issue, and they will be expensive, but not so much as your comprehensive layout redevelopment.
There are, I think, two issues. One is to remove a pinch point at Basingstoke and the other concerns electrification.
Regarding the congestion. At the moment there is a roughly hourly service of container trains in each direction, these were one of the driving forces for the recent grade separation at Reading. The next bottlenecks which will have to be dealt with are the Didcot/Oxford corridor and Basingstoke. There is already a suggestion on the table for grade separation at Basingstoke, in part because the southbound container trains off the Reading line currently cross to the Down Southampton line at the eastern end of the station. As the trains are long and the crossings severely speed limited this movement effectively stops the job for five or six minutes each hour as the Southampton track is the southernmost of the four and the trains have to cross the whole layout.
Northbound container trains towards Reading also have to slow for the junction turnout and sometimes have to wait for the half-hourly Reading shuttle to clear. This means that the Up Slow Line platform is also occupied for longish periods.
By shifting the point where the freights join and leave South Western metals to the
west of the station much of the difficulties could be eased. The trackbed through the station already exists, being the end of the old GWR branch from Reading, and there are engineers sidings extant to the north of the line extending more than half a mile further west.
The only major thing preventing the track being relaid is the pedestrian exit to the car park to the north of the track from the platform serving the Up Slow and the Reading Bay. By extending the passenger subway by a few yards to the car park the container trains could run unhindered past the station and join the Main Lines to the
west of the station. Ideally in the Down direction this would be grade separated, joining the Southampton via Eastleigh route near Worting Junction. In the Up direction a turnout from the Up Southampton line between Worting Junction and the station could lead straight to the freight avoiding line.
The electrification issue is different. If the Southampton via Eastleigh to Basingstoke section is converted then there is no alternative than to kit out the station area with both systems. However as I understand it there are now suggestions that this conversion will cause no end of issues and as an alternative wiring the route from the Southampton container terminals via the Laverstock curve at Salisbury to Basingstoke is being considered. This solution would cause less disruption and remove the freights from the congested stretch from Southampton Central, through the tunnel and up through Eastleigh.
By adding about 3.5 miles of a fifth track, electrified at 25kV, from the Salisbury route at Battledown flyover to Basingstoke for use by the freights, none of the station area would need dual electrification and the freights would be kept out of the SW side of Basingstoke station completely. The need for grade separation for the Eastleigh/Southampton route would also be eliminated.
I suggest that this would be a cheaper and less intrusive solution than a new flyover and a dual-voltage station.