Where the hell is that number pulled from? Firstly, 600 miles is not the length of the CR system, it's around 450. I have no idea how you get 600, that's way more than you could possibly have just in yards/depots. Maybe if you count each track as separate? That's more than a little disingenuous. Secondly, even if we take that 600 mile number at face value, and use the Caltrain Modernization program as our cost reference, which is absolutely insane and should not be the baseline since the project was generally mismanaged plus they got shafted on rolling stock costs, paying around 30% more compared to the MTA/LIRR for example, we still come out under $30 billion. (Not by much, it's around $27 billion, but still.) If we use the costs of the NE Corridor Electrification in 2000 as a baseline, we get $4.5 billion instead.
Given that they say "388 route miles, 650 track miles", I assume that they are counting each track as separate. Which I don't think is actually that disingenous -- wire cost is 1:1 per track mile (at least just in terms of the physical wire itelf), the catenary "poles" also increase in size and material if they cover multiple tracks, and the underlying electrical demand also increases with parallel tracks, since you can run that many more trains.
I haven't checked your cost figures for Caltrain, but honestly that sounds like it's probably exactly how they came to their cost estimate (for better or worse). Particularly in a verbal presentation, and one where they are explaining why they are forgoing plans for systemwide electrification in the inital build, saying "$27B" would imply a higher level of precision than is actually accurate, so rounding to "$30B" is more accurate overall.
That all being said, yes, using Caltrain figures is debatable, and it seems like there is a lot of a priori thinking going on.
Also, do animals particularly care about overhead lines? I feel like if anything the birds would be all for it.
I mean, I think there are pretty obvious drawbacks. It's not the overhead lines, it's the catenary poles every so many feet and the concrete used to hold them in place, and it's the disruption from construction, both in terms of the physical presence of equipment and in terms of the inevitable runoff.
Now, to be clear, I'm not saying it's a valid justification for not electrifying tracks through wetlands. Far from it: at this point, my heretical take is that we should radically de-emphasize EISs for mass transit projects. (Imagine debating whether to use water from a fire hose on particular corners of a burning house, since the water might damage priceless paintings inside. We must put out the fire, and so we must get people out of cars.)
But the potential impact on wetlands seems relatively easy to imagine; the answer isn't to deny that impact, but to acknowledge it and frame it against the harm of the no-build alternative.
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