Maybe the foot is more level when using clipless pedals because a good pedaling technique is to try to pull the foot like you are trying to scrape mud off the sole of the shoe at the bottom of the stroke. This motion will not work with platform pedals because your foot would just slip off the pedal. So to get this motion to work it might be natural to keep the toes pointed down so that the foot would stay on the pedal.

I don't know what is going on but this is just a thought.