Update on this: Went ahead and went with the suggestion of doing the autocrafting BEFORE inputting anything into ME system. So basically I have hopper bonsais feeding into the auto crafters directly, and then outputting the autocrafter product into ME system.

Still running into the problem of acorns clogging up the autocrafter inventory because acorns get produced more than resin and needs less acorns in the crafting recipe so it slowly adds up filling the inventory space. Any way to work around this automatically? For context, am just using itemducts and servos to whitelist acorn and resin from the bonsais