> That underpass allows trains headed north from the yards not to foul the southbound main.


Exactly!

There is even a common name for this sort of thing - "Flyover Junction". I believe they were invented by the Pennsy. Or at least they were famous for them; Pennsy examples being given in many railroad engineering textbooks. In any event they are now common all around the world; especially where traffic is dense where multi-track lines join. Right here in the Bay Area, even BART has three flyover junctions (two flyover wyes and one standard four main track flyover junction to two separate double track lines).

As to multiple tracks into yards, in the case of BART, three of their four yards were first built with only one set of yard leads, albeit each with two tracks. But even that proved inadequate, thus at all but one yard, a second completely separate set of yard leads have been retrofitted in. But at one location, even with two separate set of yard leads, bottlenecks still occur; motivating several failed attempts over the years to build another flyover junction.

This is a common problem experienced on most transit systems, and even on some freight lines. If anything: in the future, that Seattle yard entrance will still prove inadequate, as it is now configured.