From these numbers, and from watching them play, the logical conclusion is that D.C. United pressures shooters on the ball, and gets defenders behind the ball, to the extent that they force opposing teams to shoot poorly, resulting in missed shots, blocked shots, and shots that are easy saves for the goalkeeper. Put another way, their defensive pressure causes teams to shoot at percentages below what expected goals models would predict. That D.C. United's defense leads to a high save percentage also means that their PDO will be a poor measure of how “lucky” they are.
As further evidence that this is not just luck, teams that consistently force a lot of blocked and missed shots also tend to be teams that allow a high proportion of shots from crosses. D.C. United and Real Salt Lake, 2014's two most over-performing teams, were also the two teams that faced the highest percentage of shots off crosses. This suggests those teams are making the conscious decision to pack the box and pressure shots, at the cost of allowing space out wide.
Most teams can be considered “good” defensively by the number of shots they give up. A low number of shots typically means a low number of expected goals, which in turn means a low number of goals. Other defenses are considered “good” because they only give up low percentage shots. They may give up a lot of shots, but, because those shots aren't likely to go in, they have low expected goals totals, and they don't allow many actual goals.
D.C. United's defense, as I've tried to show, takes a third way. They give up shots, from good positions, but because of their abnormally high defensive pressure, those shots are more likely to miss the target or be blocked or saved, and therefore expected goals models overstate their chances of going in. Because of this, most metrics will systematically mis-evaluate the team's defense. This was the case last season, and it is once again the case at the start of this season. Presumably, expected goals models that incorporate defensive positioning would more accurately describe the team's defensive performance, but until the day comes when that data is made publicly available, we won't know for sure.