National labs are a tiny (and highly sought after) sliver. In my experience of rummaging through public wage records, I have never seen a staff scientist at state run university outside of the $60k-$80k range.
Yeah, he's probably paid around 140k. (Given his age [0], and knowing that first year scientists at similar places start at GS-13, I'm going to guess he's at a GS-14 equivalent with DC area locality pay.)
This, plus your internal grant money not only covers your salary but overhead, means a 140k person costs 300k or more.
Federal scientists are typically paid through a few projects that total to 100%, so I doubt all of the 462k from the article went to paying him, but probably a large chunk of that did.