That's the expected behaviour for CREATOR OWNER, and it is unlikely to have ever been any different; I think the addendum to the article is misleading in that respect. In my experience, it wouldn't usually be a problem, because you don't usually want to add stuff to the user's folder anyway. That's probably why the original article never mentioned it.
If you aren't going to create each user's directory in advance with explicitly chosen permissions, then as far as the group policy goes, you only have two options: if you set "Grant the user exclusive rights" option, they get full access to the entire folder and contents, but nobody else does; if you don't set it, they only get access to the content they created themselves.
If you go with the first option, you can use backup privilege to bypass the permissions whenever you want to add content. This is elegant, but can be inconvenient because the built-in tools for using backup privilege are fairly limited.
If you go with the second option, you can change the permissions on the user's folder before you add content; or you can explicitly set the permissions on the content that you're adding.
Another approach (as you suggest) is to use a group policy logon script to change the permissions on the user's folder when the user first logs in. This may be the most convenient option if whatever process is adding content to the user's folder isn't under your control.