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I'm pretty sure you can do this with pure botania. A drum of the wild (i think) will activate when hit with a mana pulse, and break all flowers/etc except for botania generating/functional flora
pretty much your choices are smelt it to get one apatite out of it, maybe use MFR's fortune smasher which requires Mob essence, or some contraption that involves autonomous activators placing the ore and breaking it with a pick
pretty much any type of block placer should work, i like using block placers and having the wither immediately fall into a mystcraft portal into some sort of wither proof room so it doesnt break the block placers each time