A very large chunk of the Sound Transit 3 cost will be interest paid on borrowing. Because Washington State has no state bank or infrastructure bank, Sound Transit has to "borrow as it goes" by issuing bonds, building, paying back, issuing more bonds, building, and so on. It doesn't get the funds in one up-front chunk--like Vancouver did for its light rail system, from the BC and Canadian federal governments--so it's fund-as-we-go.

Above ground does matter. Grade separated still mostly works from a transit perspective, but there are other concerns: how they affect surface traffic, how they can be affected by marine traffic, etc. Underground is more expensive but still demanded for a reason, and we are still paying >2x per mile for above ground vs what Paris paid for underground lines.