I'll bet the change was both subtle and slight, if at all.

It probably was a fatigue crack that propogated. With a waste gate controller the boost was staying close to normal, if not normal, but because it was working to build pressure the compressed intake air coming out of the turbo was waaaay hot. The reason for the intercooler is to get the air more dense by cooling it, but the intercooler can only get rid of a certain amount of heat, so the intake air charge temp was seen as too high by the sensors.

The net result was there wasn't enough air molecules to complete combustion so Jack saw the puffs of black.

If I had a wastegate and controller on either of my coaches I never found it. I suspect that is an addition required by the EPA requirements and it regulates the exhaust going into the turbo to maintain the intake manifold pressure.