This is somewhat older news, but still interesting. It's the same line that had a horrible collision earlier in the year killing 51 people.
There are a couple of standout points to me:
1. It is surprisingly cost-effective as a means of grade separation. The 52 grade crossings for vehicular traffic would, in America, typically cost somewhere around $70 million each, and an additional several million for each pedestrian crossing. Even then, this would not entirely prevent pedestrian strikes or vehicles interfering with train traffic, though admittedly, it likely doesn't matter statistically. Of course, American tunneling costs are also quite a bit higher. I suspect that much of the cost with this project is due to relocating the fifteen stations underground, though building the tunnels large enough to accommodate bilevel trains undoubtedly plays its own part in it.
2. There is an absolutely tremendous amount of traffic on that line. If I'm not mistaken, the ten million passengers per month on that lone 35km line is three times the number of passengers on all California commuter rail lines combined.
3. This also appears to be part of an upgrade for the line in question, renewing its electrification and signaling systems. Currently it appears to be using electric locomotive hauled single level equipment, which heaps even more shame on California's commuter lines. Since the equipment on the line will be sixty years old by the time the tunnels are completed, and aging equipment has been blamed for the earlier collision, I don't think that the double deck height of the tunnel is simply future-proofing: I would be highly surprised were there not to be a double deck EMU contract timed with the new tunnel openings.