It seems like an overengineered solution. A robot arm with image analysis? Why not just stick the apples in a hopper, put in a little door to release one apple at a time, and then just move the hopper back and forth (using a Python script) on a track along the line of crates?
You could also attempt to build a purely physical apparatus sans code to distribute them randomly, but it would take a lot of work to prove it was unbiased. The best solution might be a roulette-wheel style arrangement where the apples are emptied into the middle and move out towards the edges as the wheel spins (you might want to make the crates counter-rotate as you did this). Not bruising the apples might be a challenge.
You could also attempt to build a purely physical apparatus sans code to distribute them randomly, but it would take a lot of work to prove it was unbiased. The best solution might be a roulette-wheel style arrangement where the apples are emptied into the middle and move out towards the edges as the wheel spins (you might want to make the crates counter-rotate as you did this). Not bruising the apples might be a challenge.