"Bark side down" has the deck board oriented so the end grain growth rings curve upward. This creates a crowning warp when wet. As a result, water is shed from the board as opposed to pooling in it. Also, the exposed board face is heartwood versus sapwood and heartwood is more decay resistant.
The only reason I can see to be careful with this deck board orientation of bark side down to avoid a defect called "shelling" as mentioned in the previous section. Shelling is a raised grain defect where late wood growth separates from early wood growth and creates a flat splinter-like defect after repeated wetting /drying cycles and is more common in Douglas Fir and Southern Pine lumber. But just be select in the pieces of lumber you select to avoid this problem.
This orientation of bark side down is my preferred method because it avoids the unsightly trip hazard of cupping.
