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And what "seems" badly flawed seems so based on a long cascade of vague assumptions.  How much a person values (say) the rookie Adam Jones depends on an incredibly complex set of variables, such as the delta between Jones and whoever winds up playing CF for the Mariners in his six club-controls years.  We can't even delta Jones against the minor leaguer behind him, because trades are part of the fundamental rules of the game.  Shortly after Adam Jones left, Franklin Gutierrez was posting 5.0 WAR and had been acquired for next to nothing.
USSM flatly stated that Adam Jones, by himself, was worth far, far more than Erik Bedard even if Bedard pitched at the max of his capabilities and even if Jones did not play well, because the assumption at the time was that any club-controls 2.0 WAR player was worth more than any MLB superstar signed at anything close to market value.  This led to two years' worth of the incredulity you speak of, but they lost their incredulity when the roles reversed in a Cliff Lee acquisition.  The point is simply that what "seems badly flawed" seems so to analysts who have only a tiny fraction of the information they need to "value" a player "correctly."
As James remarks in situations like this, "We don't have near-perfect measurements of baseball players.  It is foolish to assume that we do."  
Respect for the complexity of the problem is part of the SSI community standard, as is respect for other posters' ideas.  Everybody here is as smart as you and I are.  A specific and detailed set of arguments against [Position X] will impress the community far more than will incredulity.