yeah.
Though that won't be the only thing affecting the tone- a floyd sounds different from a vintage strat-style bridge, or from a tune-o-matic, a necth-thru sounds a bit different from a set neck or bolt-on, etc. etc.
How do you like the tone of your neck pickup? IIRC it's a duncan '59, which is a vintage-voiced pickup. If it sounds good to you, then you could probably switch the jb out for something more vintage and be pretty pleased with the results.