First off, the WAR you are quoting is not batting WAR, it's overall WAR. According to bWAR, Machado did outperform Xander overall last season. According to fWAR, Xander outperformed Machado. In terms of offense alone, both fWAR and bWAR have Xander outperforming Machado, although Machado did better in wRC+.
At any rate, my post was in response to your statement that "A bad year from Machado blows away a good year from Bogaerts." That is simply not true.