Pure speculation but it seems to me that with these guitars they do choose tops from the available 10-tops, they can pick the ones they like best, but the neck/fretboard do/must come from the Wood Library (it does still exist AFAIK, its the Private Stock stash) - they don't even use those woods in Artist Packs let alone Core models. And then perhaps there are instruments where only the top comes from the WL but the other woods come from the Core supply room? It seems to me that these WL guitars, being half to a third of the price of a PS build maybe can't be 100% PS materials, but can partially be and that's the USP. It's a bit, uh, opaque.
Theory number two is that the tops ARE from the WL but are maybe the "B-grade" Private Stock tops (heh), and because the WL grows over time PRS feels the need to 'thin out the herd a little' and these WL runs allow them to do that. So they pick out the "worst" of the PS stash to allow dealers to pick from. Which is to say, it's still exceptional. Maybe the '10' is simply added to differentiate it as a regular Core model and not a custom Artist Pack.
As far as your second point, tops change too when they are carved and sanded... sometimes they change the grade afterwards, but not always. So one that might have looked spectacular as a blank might be less so in finished form, because there's no way to know exactly how far down some of that figure goes. In addition, some colours seem to amplify or even subdue figure more than others. Otherwise I think there's just some subjectivity about consistency of figure, what looks "good" and the fact that the graders "just know."