Your mechanic's line of thinking is what leads people down the road of chopping up the insides of their airboxes for no good reason and other stuff like that. I'm curious why he replaced the timing chain? Hopefully not for a lumpy idle?
The intake is not too small. If the intake were sonically choked, it would impact wide open throttle, not idle. Think about how the throttle works: closing off air to maintain stoichiometric combustion. That butterfly valve is pretty nearly closed at idle. I do believe the intake manifold has too little volume. But that impacts throttle transients, where there is a sudden increase in vacuum. That's why the spacer works, or why I think it works. Doesn't mean Nissan designed it wrong, as there are other characteristics in play. But that's different than the intake being too small.
Anyway, "rough idle" is subjective, but I believe my V-6 is really smooth at idle and I have a much older truck (182K miles) with polyurethane motor mounts.
I'd consider the MAF sensor as mentioned above. Another thing you can do is try the idle air re-learn yourself. It can be done with a pedal dance, but I have an easier way. Look for an app called Nissan DataScan II in the Android or iPhone app store, and get an OBD II Bluetooth dongle with an ELM327 chip in it. Aside from being able to read Nissan specific ECU data, it can also perform the idle air re-learn at the push of a button. That does smooth out the idle a bit, especially if you've changed a bunch of things like plugs lately. If this was a non-Nissan dealer, they probably didn't do it.