I actually don't use the forestry multi-farm for this specific reason. There is an apatite bee now from extra bees, so that will help, but you have to research bees to get them.
Most of the products that a multi-farm would produce can be made in multiple ways--Thaumcraft golems being one of the preferred methods. Peat can be made with redpower or another mod that give a block placer and a block destroyer along with vanilla pistons. Cocoa can be had from bees or MFR farm, and mushrooms can be farmed with vanilla or MFR. The only type of farm I can't produce using other methods is an orchard, so if I ever breed some fruit bearing trees, I might make one of the multi-farms then.
The latest versions of forestry have lowered the height that apatite spawns down to around 64, so it should be a lot easier to find.
Edit - I would like it if the farm would take mulch or compost as well, but it would be less efficient than apatite. Since both of those can be made endlessly with some automation, it would be worth setting up complex interactions to make all of it happen.