When you do it, just thread the insert and not the wall of the head. Drill through the insert and thread the entire hole. Drill the hole in the head so that the shaft of the bolt is snug but doesn't thread to it.
This way you can tighten the bolt in a way that it clamps the insert to the head and you are guaranteed that the bolt hasn't bottomed out in the insert.
If the tip of the bolt sticks out a little into the port, that's ok. It won't adversely effect anything.