Relation of rebound setting and pedal choice I used to ride clipless pedals all my MTB life and have recently switched to flat pedals because I feel that having my feet free makes me experiment more with my riding technique and progress faster. I have ridden a very quick rebound all the time and felt comfortable with it when riding clipless but when I switched to flat pedals my feet were kicked out of the pedals. I've adjusted to a slower rebound and feel comfortable now.

But this makes me wonder what the correct rebound setting when riding clipless is. Should it be set as if my feet weren't attached to the pedal? Or is the idea that you can ride a quicker rebound since your feet will stick to the pedals anyway? (of course only as long as the rebound isn't so strong that it kicks your body to the bars)
There shouldn’t be much of a relationship.

The rebound should be set in accordance with the total rider mass and the terrain. You want the fork to extend quick enough before the next depression in order to take better advantage of the full stroke.
So if you have more up and down terrain, higher speed or a heavier rider, one tends to set the rebound faster.

I suspect that the flats have simply highlighted something that you can improve on in your ‘pedal’(standing) technique. When using clipless, it’s very easy to unlearn how to ‘pinch’ the pedals between your feet as the cleats does some of it for you. With flats, if your not holding the pedals/bike with your feet, you know about it straight away.

To exaggerate, in order to explain. From the normal level pedals position, take the leading foot and point the toes down. Now on the back foot drop the ankle. You can now pull the lead foot back and push the back foot forward and this will allow you to ‘pinch’ the bike with your feet. Try it in the parking lot, moving slowly and you’ll find your bunny hops improving as well. 

When you are hammering down a hill, it is curial to hold the bike with the feet, actuate the knees and guide the bars. Setting the rebound to keep your feet on, means your foot work needs practice or you rebound setup is way wrong.