From what I know of the 2-stroke diesels EMD has used (maybe different with newer models and EFI in the mix), is that they used a clutch system for the turbo. It's directly coupled to the driveshaft at lower RPMs, then once exhaust pressure was high enough, the clutch disengages to let the impeller free-wheel.

An interesting anecdote is that some shops would lock the clutch in place, 'de-rating' something like a GP39 (645 turbo) down to the equivalent of a GP38. (645 roots blower)

As for the Alcos, I think the early (S1, RS-1/3) models had some sort of mechanical governor that managed the turbo, so thus you end up with severe lag if you don't keep everything adjusted just right. As long as the loco continued to run, a little extra smoke wasn't considered a problem. They *can* burn clean, it just takes extra work. :-)