Crazy.

My guess as to what happened: Diff housing was not replaced. Tech was familiar with the issue and instead of replacing the housing and bearing they just installed an ECGS bushing, and during removal of the bearing they managed to damage it to the point they lost some of the rollers inside the housing without noticing (ie they had rollers all over the floor of their bay and assumed they all made it to the floor).

Perhaps the casting or machining of your diff housing is far enough off that even with the bushing there is enough play to cause the sound, or maybe the axle shaft is a few thousands smaller than it should be, or it could be something else completely. Did you say the noise goes away in 4wd?

As far as the bearings being on both sides - yes, they are on each side of the carrier, however on the passenger side, the CV doesn't go into the carrier. There is an intermediate shaft (41304F) that runs from the carrier through the tube (part 41320) and that shaft is supported on the other side by another bearing (part 41304L), so it is near enough to perfectly straight with no side loading of any kind.