I think that TODO comments might be used in many different ways by different people.  A notification would help me, because I generally don't want to check in code with unfinished TODO items.  For many people, I think having it off by default is a good idea.  Perhaps it could be a a notification with a checkbox for "Don't show me this again" option.

That's a good point. The IDE I'm using nowadays isn't as sophisticated as IntelliJ (or other JetBrains' products). That's actually why I bought SmartGit, because it provides the git features that the IDE lacks.