Anyways, after poking around with Immersive Engineering's splitting conveyor and finding out that it handles hopper-inserted items a lot more consistently than hand-dropped items (when I tried the latter it almost always pushed everything in the same direction), I ended up going with that.
On a related note, my Botania tree/munchdew farm is a mess. A hilarious mess, but a mess nonetheless.
If you turn you Munchdew into a floating variety and stick it up in the air so there are leaves below, it'll only eat up from there, so you can get saplings as well as generate mana. Combine with a Gourmaryllis to eat Apples if you're growing Oaks.
I have the Munchdew set so that a portion of the trees are outside its radius. Adding a gourmaryllis for the apples isn't a bad idea, though trying to figure out how to get both the apples and the shutoff signal to it is probably going to be a pain.
Unless you're using them for food, Apples are a by product so wasting a bit of mana isn't really going to be an end of the world scenario. And it'll stop working when there aren't apples, so it'll stop working when the rest of the farm stops if that's necessary. IE if the tree's aren't being harvested the flower won't run because there aren't any apples for it to eat.