I agree with much of what you say. And I'm a bit suspicious that, at this late stage, it has suddenly been realised "Oooh there's a lot of chalk there so it will be more expensive than we thought"!
I also think "only the best will do" and thought, if there has to be a tunnel it ought to be the long version not the cheapo one that you know who were supporting.
Perhaps this could all end up as a blessing in the end though. Compared with the quoted cost of a tunnel, wouldn't a bypass (say £40 million per mile??) start to look attractive?