With the Pod, certainly one can discern the difference between pickups, regardless of whether they're bareknuckles or others... it's nore noticeable with the Pod than lesser-quality gear like a V-Amp, yet today's modellers seem able to retain "transparency" of things like p/ups and the inherent "tone" of an individual guitar.
I've also found that the better the pickup, the better the sound that comes out the other end...amp or modeller!
True, the nuances of guitar volume/swells are not done very well by modellers, and for a true reflection of anything that uses sound, one needs to have the sound go through real air as opposed to the virtual stuff: so, yes, better pickups do make a bigger and very noticeable difference with better modellers like a Pod...and an even bigger difference through a real amp.