And when there are plans to re-electrify the rest with OHLE in the next 40 years or so it does not count as an infill because it will be ripped straight up again before it's life-expired. It is not a waste of resources when it saves us money in the long-run. That's to say nothing of the fact that it won't be electrified with any system until other lines that it would electrically interface with (for example, at Farnborough) are also being converted, making it natural to switch things over.
There are plans to have colonies on Mars inside 40 years, it doesn't mean they are going to happen.
People complain that there are too many jobs to do with far too few resources, then go and invent dozens of additional jobs that they want to expend resources on because of marginal cost savings.
In other words we end up with a diesel railway for 40 years when it could have been electric, followed by the realisation that the fabled conversion probably won't happen anyway.
And we have more than 40 years worth of electrification work to do even without any conversion projects, so North Downs or similar lines could simply go to the back of the queue. After all, as you said, changeover on the move is not really a big issue.
The primary difficulties of third rail arise in high demand, high traffic areas.
The North Downs is not one of these.
Network Rail are not intentionally out to lose money, and are not fanatics that hate 3rd rail simply because it is 3rd rail: there are very real and very important practical and business reasons to not use 3rd rail anymore.
None of which apply in a particularily strong sense to the North Downs or similar infill projects in the South East.
We are not talking about the SWML or the Approach to Waterloo (and I would love to see a practical OHLE layout for that, 8 track gantries will be rather amusing, especially getting the total line blocks to put the damn things up).