Tunnel boring, digging and other soil/earth works are the big cost factors, the required logistics, and regulatory processes (permits, permits and making sure that you have a plan when you close important lanes on streets and avenues of a big and busy city - so traffic engineering).

The crossovers probably cost so much because they're underground and require extra tunnel space. (They require extra (as in between the two-or-more tracks that are being switched) foundations above ground too, which is probably more expensive than the switch itself.)

However, I'd like to see a cost breakdown.