No, it's a bug!
I called Google device support yesterday on the WiFi sleeping issue, and told them that my third Nexus 4 phone had the same defective WiFi behavior as the previous two, as described in previous posts here. Then I asked to escalate the issue so that I could talk to a level 2 support rep.
The rep was quite helpful and put me on hold to talk to some of the Nexus 4 software developers. She came back and said that the developers told her that this "deep sleep" turning WiFi off behavior was actually a feature. I told her that it really acted a whole lot more like a bug, in that it breaks the Advanced WiFi Setting for keeping WiFi on "Always", and asked her to feed that back to the developers. Not to mention the fact that turning WiFi off basically bricks the phone until you manually wake it up again...
So, the good news, I guess, is that it is not a hardware problem. You'd think that after 2 RMAs, though, Google would have known this and simply shared that information right up front. Now that we know, however, those of you experiencing the same problems should call Google support and provide feedback to them. The number is 1-855-836-3987.