Thank you so much for bringing up that glowing report.
Quoting: "The car was running high boost and advanced timing - enough to make it detonate when the non-intercooled air hit the combustion chambers."
I suspect the detonation heard by the writer was actually pre-ignition, which occurs before the spark event, and is caused by excessively hot combustion chambers. This form of abnormal combustion cannot be controlled by retarding the spark, so the J&S is not programmed to listen for it.
I saw this on one of my first installations, which was a non intercooled 7psi Paxton blower kit on a '92 Mustang. In individual cylinder mode, the unit would control perfectly for about three seconds, then audible detonation would set in. My scope showed audible knock was happening several degrees before the spark event. Switching to retard all mode, no pre-ignition, and the unit controlled well. Thinking back on my Beta software, I had a more aggressive retard profile in individual cylinder mode.
Too much retard can heat the exhaust valve, leading to pre-ignition. For the Paxton installation, software would retard 2, 4, or 6 per event, up to 20. The test software used in the Paxton installation also added more retard if in individual cylinder mode. This may have been too much, actually causing pre-ignition. Production software removed this "feaure". Later units incorporated the mode switch to select 10 or 20 max knock retard.
The unit pictured in the article has the range control switch, but I don't know how it was configured. Probably set to 20, since that sounds like the right thing to do. After all, it's still pinging, right?
Note that the 20 mode is still useful, if things are in reason. For example, this mode was used on hundreds of early Sebring/Jackson Miata kits, which had no intercooler, but did have rudimentary (RRFPR) fuel control.