With the Orchard the leaves are never broken. The tree just stands there, only apples are produced, no saplings and no woods. The managed arboretum, on the other hand, continually chops down trees and gets you apples, saplings and wood. It also turns the dirt into sand that you have to pump out, and thus you need to feed it more dirt for it to continue working. Generally speaking, if all you want is apples, Orchard, if you are going for a biofuel setup? Run the Arboretum. Gets you everything you need to start producing biomass and turning it into biofuel... Apples are squeezed into apple juice, which is better than water for fermenting, saplings to turn into biomass, and the mulch you get from squeezing the apples to run the fermenter. The wood you can turn into charcoal and use it into a secondary solid fuel boiler.