There’s a proper riding position and cockpit regardless of whether you’re riding clipless or flats. If it causes you problems when riding flats, it’s not that it was right while riding clipless, you just didn’t notice since your feet were attached to the pedals.
The only thing I’ve heard or read being different between the two is that some people ride with their arch above the axle instead of the ball of your foot. Personally, I found that impossible when riding xc, due to the pain it caused miles in. I ride with the ball of the foot over the axle, regardless of the pedal.