These are some really important issues about Xabi Alonso tactics and recent loss to PSG. Team defense clearly has problems letting in four goals. You are right that having too many attacking players can make defense weak. It also looks his three defender plan is not working, showing he is still trying to find best way to use his players to make them strong everywhere especially in defense. It will be interesting to see how he fixes these defensive issues.
Enrique is right to understand Xabi's situation with Madrid. Most observers will know that during the semi-final, they didn't have a pure center-back. Rudiger didn't have a defensive partner, and he even made an error that led to a goal. I think Xabi kept racking his brains to get the ideal composition for that semi-final. In the end all plans failed and indeed PSG were much better. Now Xabi must think ahead. The condition of the team seems to be not ideal as long as many players are injured. Xabi may be able to add more players to the defense to face next season with a busy schedule.