The top window bar (titlebar) should NOT overlap the movie. At all. Ever. It overlaps the area where we often do timecode and other data burn-ins.
It should only do this when you "hover" the cursor over the QT X Player display area. As to "At all. Ever.", this is a user-to-user forum and you need to provide Apple with such feedback to request an "enhancement" option to disengage or change the current convention.