To help BA744fan get back on topic, let me state from professional knowledge that the Emirates A388 has 4 seats across in business on the upper deck.
They achieve this by using different pitches on some seats, giving a two class cabin.
But it is 4 across, end of story.
Now to the original question, my guess is that the upper deck would be preferable, so long as not in the ‘coffin’ middle seat, in the bank of 3.
Preferable because the two upper cabins will feel less like a dormitory than the main deck.