The one thing I left out of the article is tackling the problem head on. This may not make sense with every manager, but it could be worth trying:

Adding an intentional flaw is not addressing the core problem. Consider talking to them directly, pointing out their behavior, and try to get them to only make valid changes. Not just to leave their mark on the design.

Like I said, this may not always work, but it is better for your long term relationship with your manager.