Well I tried to create a small automated system for it, and it worked like a charm. I think it could use some refining, but the concept is sound. It does run you into the obvious issue of Vis cost for the process (the wand has charging and the pick has repair 2 so they are self repairing at the cost of further increased vis use). It does a strange thing with the bore head where it flails wildly around for a second before and after breaking the iron ore, nothing just a visual however. The final thing I am looking at is if you do have 100% of the ores turned to native cluster than how far beyond 200% does it go and is it worth the effort, and it looks to be about a total of ~216% with 3 arcane belows on the infernal furnace, so it depends on the person if this vis cost is worth an additional ~16% ore output. It isn't spectacular but it is still an improvement beyond the normal output range.
While testing this on my own, I stumbled across something interesting. I forgot to aim the bore up, so it immediately harvested the deployer which had a stack of iron ore. The bore ejected a stack of native clusters.
Here's my variation on your design. I think I've made it as small and automatic as I can.
http://i.imgur.com/rvPEYHG.jpg?1
The optimal timer speed is 5.50, and the Buildcraft gate is set to "Inventory empty -> Redstone signal". The advanced stone golem has all six cluster-able ores assigned to be moved from the chest to the deployer. Drop ores into the deployer and it automatically "converts" them to native clusters.
Edit: Just realized another use. You could also easily use this setup with any silk touched diamond blocks/emeralds and a Fortune pickaxe in the bore. Also, it's a gravel to flint converter!