Yhea you're right, I usually think of his tones as compared to the guitars. But still, I like the super II in my guitar. I also use Dmarz 36th anv PAF's and love the tone with those too. My strat I use the Area 58's, perfect old school late 50's strat sound. It still seems possible to come close to his tones with different makes and models of pickups with dialing the amp, but the super II has a bit more twang in split mode much like my strats twang, but the super is much more sensitive to dynamics. I have sat here listening to Althea from 1981 and 1983 back an forth, most people would call us crazy for noticing a difference, but there is. It is so slight, that it could be achieved through EQ and amp settings. Even a change in his playing style will give us a new tone to identify, let alone a change in his pickups/guitar/gear.
This is an interesting question because when I think of the tone I like and what I emulate are two different things almost. I haven't really worried about getting things exactly like his or an exact era, I just like his overall tone, the basic bedrock to build on. I use a lot more dirt than Jerry ever did, but his twin sound with a split super II is a great tone, the twin/JBL is what I take most from him, since I use other guitars too. I have gone back to older set ups to do some A/B comparisons and I can't believe I haven't done this all along. I guess I use a hybrid of his tone and I particularly like 1975-78 and the early 80's