Your GT500 problem sounds like valve noise.
If your truck is knocking as much as you say, it would have thrown an engine light long ago. It doesn't sound like knocking either, esp. since it's occurring at idle. Could again be valves, but since you say it's low in the engine, maybe a bad water pump? Then again, could be any sort of rattle. Not likely knocking though.
Your tuner would more likely show a modulation of boost pressure before it retards timing.
People think that well, it's a high compression turbo so surely it needs high octane. But remember that a high compression turbo doesn't have to produce high pressures. Open the waste gates and it's gone.
The advantage of higher octane is that the waste gates won't open as much. The engine will allow a higher boost level, and you'll get more power. At the cost of worse economy, of course. But running low octane fuel isn't going to damage anything - you just won't get as much out of the engine as someone who does. Knock sensors and knock prediction won't let you damage the engine.
At what point the boost throttling happens - now that's an interesting question. It won't be idling in the driveway, and probably not tooling around town. It's probably going to show itself only at higher RPMs and big boost - trailer towing, highway on-ramps, etc.
