I like what Erik said in one of his comments starting with the "I'm confused...". One of the tricks I believe in dealing with bosses is making them feel like they make all the decisions, know everything and are the greatest bosses in the world (stroking their ego is what I like to think it is). One of the tricks I use to do this is sometimes make myself seem like I don't know what is happening when I notice something "I believe" is wrong (it may NOT be).
This is leading on from Eriks comments. Sometimes I'll say things like:
I'm struggling to grasp this code. Can you talk me through it.
We have started implementing some processes that will help make our team more productive in the future. I'm not sure how this new code fits into that. Can you talk me through it.
Is there any reasoning why you did this like this? We have some similiar setups that we are working on that might make this easier to implement in the future.
Sometimes we just have to put up with the "interesting things" that bosses do. Some bosses find it hard to step away completely and really enjoy getting in there. However they don't like to believe they are no longer required and sometimes don't want to show their inadequacies in case they feel the team might lose respect in their abilities.
Basically, try and make your boss feel like the changes he did was really helpful but you don't quite understand how they fit into the direction that the boss and your team is trying to follow.
If your boss has insecurities etc you may have to just be prepared to have to review all his code and try and fix/change them without his knowledge after he has made it.
In the end, you can make suggestions and talk to your boss, but you can't change his way of working. That is up to him and his bosses.