I read on some guitar tech's website that he didn't recommend potting Jaguar pickups because they lose top end but that never happened when I did mine. The sound remained identical, I even made a recording before and after to check. I just lost the squealing.
When you think about it all you're doing by potting a pup is stopping movement of the hardware both inside, and in my case around, the pickup. Since a pickup is not meant to have moving parts (the moving string makes the current flow in a static coil) why would potting it in any way change the tone? The wax itself would have no effect on the magnetic field.