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A Botania-only solution:
Hopperhock and redstone powered open crate. The redstone signal on the open crate will prevent the hopperhock from picking up the dropped items until they get transmuted.
Hopperhocks from Botania also have a filtering feature - place the item you want to pick up in an item frame on the inventory your hopperhock puts items in. (not sure if it works with ME interfaces and such, but it definetly does with vanilla chests)