Reading the IMCHandler code, I should be able to do this:

FMLInterModComms.sendMessage(modID, "registerHarvestable", new AppleFactoryHarvester());

and all would be well in the world.

Unfortunately, not so, forge has no overload for Object OR a visible IMCMessage (so I could send it manually), only String, ItemStack and NBTTagCompound, therefore, any code that would take arbitrary objects is essentially bricked by design.

Please do correct me if I'm missing something here, but how would I send a IFactoryHarvestable through the IMC if it won't accept the Objects through its interface?

FactoryRegistry.sendMessage("registerHarvestable", new AppleFactoryHarvester())

(This class also documents the available messages)