[Bleeding] Ignore Block Physics in Chunk population. Fixes BUKKIT-4923

Suppressing physics updates during Chunk population prevents
infinite recursion due to custom Block Populators editing border
blocks on chunks.
Don't consume bonemeal if there is no crop present. Fixes BUKKIT-3790

Bonemeal dispense behavior already took care of decrementing the item
stack, therefore we shouldn't manage the size manually.

Pulled from PR #1172