As I said there are clearance issues, here. But, I still wouldn't want "go down" here. Where you're at "water level" next to the river, in the overflow flood plain, with high ground water in this area. So you'd need a lot of pumping infrastructure and possibly even a flood protection system.

"Going down" generally costs significant more than piling up dirt and "going over, which is maybe why so many get chosen....where higher costs generally will equal higher profits for the contractors...under our system of free enterprise...and "our" choices in these often political decisions....

I'd actually look at the cost to replace and raise the fairly old Slauson Bridge, which has a lot of clearance now (just not enough for both lines), which has long approaches presenting gradients that could easily meet the clearance, and still go up and over with the choo-choo line. I'd look as that as an alternative to "going down" under, and see how each of those alternatives pencil out.