This is the attitude that Network Rail appears to have had with Steventon bridge and Cardiff Central. While they don't avoid the 'problem' entirely (as can be seen by the fact their excessive destruction was stopped at Steventon) they seem to be pretty confident of getting approval from the planners. I still fear for Cardiff Central - extensive demolition is still on the cards as far as I know.
Having now had a bit more time to think about it, I must admit that some counter-examples have now come to mind, where parts of a listed structure have been saved during demolition. I maintain however that their proposals for both Cardiff Central and Steventon bridge showed a lack of care in those cases - perhaps there are different departments with different attitudes?
As far as Crewe-Chester electrification is concerned, the structures most likely to be issues (though they may not be) are the brick arch bridges and the tunnel under the canal. If the bridges require work (did Steventon require track lowering?), are much the same as each other architecturally and are not hugely significant on a national level perhaps the thing to do would be to pick one or two (where there is least flood risk) for preservation through track-lowering and demolish the rest with new thin-deck modern replacements. That's the sort of thing the listing system is presumably supposed to be doing, but it doesn't seem to be working like that (not just talking about the railway here, but society as a whole).
I suppose if you look at rail in isolation that could also be the cause. However, with one possible exception (was wiring TPE, MML, GWML to Swansea, ValleyLines and the electric spine, plus HS2, ever all 'going ahead' at the same time?) there has tended to be a good deal of capital investment in motorway and trunk road schemes (and possibly airport expansion - was there ever any government funding pledged to the Heathrow 3rd runway?)
