I have a mod that post notifications into the forum area. As I do not want all these notifications seen by my members I needed to filter them first. So I followed the following steps.
I created a member for this mod to post as.
I have setup this member to be moderated on posting ACP > User permissions > bot user > Follow message moderation rules to Never.
Now if I actually login as this user and post in the forum area that it will be posting in all the threads go into moderation as they should. However if the mod post as this member they post are not moderated at all.
You said that you logged in as the user, but we're not clear how the moderator is logging in as the user exactly.
If you actually log in as the user, there's no concept of being related to any other user, so I don't see any way this could happen. (This code also hasn't change in 1.3 and it's not something we've had a report of.)