It could work, yes. It'll be an overall bright sound, but shouldn't be harsh or thin.
Honestly though, I still think the Nailbomb is the optimal choice for you - in a bright guitar it should be rather close in sound to a RY in a dark one.
I've emailed Tim but I've also trawled this forum and researched everything so I'm reasonably sure what he'll say. It helped a lot finding a clip of a Nailbomb in a Jackson Kelly which, although not thru-neck, is maple neck, alder body and OFR so very similar. My research suggests the following about the pickups:
Emerald - Great pup, probably underused and underrated on this forum but too bright for my guitar.
Holy Diver - Can't get away from the fact that the bass sounds too flubby for me, being used to ceramics.
Cold Sweat - Had them before and loved them but that was mahogany and they're too bright for this guitar.
Rebel Yell - One of the most awesome pups I've ever heard but too bright for an SL3.
Crawler - Great tone, great pup but maybe not quite 'Metal' enough for me.
Miracle Man - One of the best pups BKP do and ideal for my guitar but too much of a one trick pony.
Nailbomb - Seems to do everything well. It seems almost like a ceramic pup from other manufacturers yet retains the warmth of a more vintage pup. It seems to be a 'Jack of all trades, master of most of them' if I can paraphrase a well known saying. I think Tim will suggest this one.
I think the choice of neck and middle pickups will be determined by the choice of a Nailbomb for the bridge. I get the impression that the Slowhands are the best for the PAF-type sound I'm after (early Dave Murray) but probably not powerful enough to sit well with a Nailbomb so I think it will be Trilogy Suites. Now let's see if I'm right :D