Mixing pickups is not a bad thing per se, and you'll find that BPKs "sets" are composed of two distinct - and sometimes quite different (magnet type, wire gauge etc) - pickups. Tim knows his pickups well and pay attention to customers feedback so if you clearly explained what you have and what you're looking for chances are his recommandation is the best advice you can get. Now if you're unsure you can always get back to him to consider another option...
I can't comment on the PK/Emerald as I never played any of them and I'm not really into metal. I have an Abomb bridge / Mule neck combo on my SG, works fine for me but the SG is a pretty different beast and I'm not sure the ABomb would match your guitar, might be a bit _too_ abrasive without the full mahogany plank to tame the highs.