When I place a bucket of water but have another in my inventory, I can't then pick it up again, because the bucket is in my inventory. So I have to turn hand restock off every time I go mining or throw away any extra buckets I have. How can I stop it from replacing my buckets?

A blacklist for hand restock is on the todo list. There is no way to prevent it in the current version, other than turning off the hand restock.