RP2 auto farm isn't really as possible unless you have a steady supply of bonemeal
Planting with seedbags and harvesting with water from dispenser is a way to go. Setup cost is really small, so you can do it early game, you don't even need to add redstone control, 3 button pushes are a lot faster than running around collecting drops, however I suggest some gates to get a few harvests without maintenance (you need to refill seed bags in deployers, but they can last up to about 200 cycles).
About apatite, you can get 24 stacks of fertilizer from one stack of apatite (normal forestry difficulty), using thaumic bees recipe and ash. One stack of fertilizer gives me about 80 stacks of saplings in multifarm (oak trees with triple saplings), so I don't think this is a huge problem. Also in newer railcraft saltpeter is renewable, but I haven't really tested this mechanics.