If they were willing to adjust their offer upward which they had indicated in the press, then the methodology was flawed. If you take them at their word that they would have moved the original offer up, that means that they had established that he was still a value at a higher price. The fact that they didn't get to communicate that to Damon and potentially retain him was bad methodology.
The Monday Morning QBing shows that the value placed on him by the Yankees was too high, but it doesn't verify that the Red Sox properly valued him, because they never got to give him a final offer. The Yankees, with their take-it-or-leave-it approach probably saved the Red Sox from over-valuing him. If they gave him time to go back to the Sox, they would have upped the ante, and using 20-20 hindsight that would have been the wrong decision. You can't give the Sox credit because another team precluded them from making a mistake. Their right decision was merely fortuitous and not the result of good business acumen. Sometimes it's better to be lucky than to be good. The same could be said of the Jose Contreras debacle. The Yankees snatched him from under our noses. He ended up stinking, but that doesn't mean the Red Sox exercised good business judgment. They were looking to give him a hefty contract. The Yankees superior networking and negotiating saved the red Sox from a terrible waste of resources. Both teams had Contreras valued wrong. The Yankees executed their plan better. Contrearas stinking doesn't make the Red Sox the better organization, because they did a bad job of executing an ill-conceived plan for a player that they drastically over-valued.