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First, that the ProspectBot can't account for college careers, at least not yet.
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It can if I want it to. I've chosen not to use college stats, because they're so unreliable (at least they appear to be), but from the research I've done, college ball appears to be roughly equivalent to Rookie league (Pioneer League, Appalachian League) for pitchers and the complex leagues (Arizona League, Gulf Coast League) for hitters (it makes sense that there would be a difference there, because hitters have to adjust to wood bats).
If I put Weathers' college career into the mix, he ends up at #31 on the Rockies' list. His college numbers are excellent, but they're not Wagner/Cordero/Street good (which in itself says something, since none of those guys were picked as high as Weathers was).
One other point here, which I thought was blatantly obvious but seems not to be: if the ProspectBot is just as good as the BA/Goldstein/Sickels lists, that does not mean that scouting is worthless. It simply means that the ProspectBot does a better job of reading the numbers than the other guys do, thereby making up for its lack of scouting input. The claim has never been that the ProspectBot is perfect, just that it's as good as anything else.