Dojii, your two main points are absolutely correct - the first one about the importance of defense in improving a pitching staff and the second one about making the moves that give the TEAM better value, not the individual players.
That being said, I'm not on board with the idea of moving Bogaerts back to 3B. Is he better suited for that position defensively than he is for SS? Probably, but the numbers, in a small sample, don't bear that out.
More to the point though, moving him to 3B seems to have some kind of negative impact on him. Last year he was a disaster. He sees himself as a SS. I am a strong believer in the idea that a player should suck it up and do what's best for the team, but if moving him to 3B is going to have Xander take 3 steps backwards, then that is not going to work out best for the team.