I have always placed the shims between the extension flange and the receiver, not the barrel nut.
I was instructed to do it that way, then learned the hard way to do so when I ignored those instructions, because the shims aren't very robust, and it's not that hard to pinch one out of alignment when you torque the barrel down.
If you buy shims produced from shim-stock, they will retain the "trueness" of the receiver extension. For what it's worth, the whole [beeep] thing has to be true together. If the barrel nut isn't true to the extension, it will produce uneven pressure between the barrel extension flange and the receiver, just as if the receiver wasn't true anyway.