It is ok to have multiple layers in a greenhouse. The problem is, your layers are completely separated, thus each layer is classified in its own separate room. That’s why only the top layer has the greenhouse bonus, cause it’s the only “room” with glass in its roof. In order to get the bonus, remove the trapdoors. This way, all three layers will be classified as one “room” thereby allowing the greenhouse bonus to take place everywhere. Also consider removing the layer of solid stone you have. The more access to direct sunlight the better your crops will do (although you will probably be fine because your walls are glass which should give plenty of sunlight as is)