ATM9: 0.0.65
There is no way of choosing which recipe I would like to use for any auto crafting system I can find (rftools, refined storage, enderio, likeley ae2). I currently am having trouble with tiny coal and charcoal, as lots of these conflicts are recipes with a single item a solution could be to make the recipes apply for only a single slot in the crafting grid rather than have them as shapeless.

Tiny coal fixed