The adaptation porocedure is just for idle. In tunecu,hitting reset adaptations sets the ecu to factory defaults. When I was using tuneboy, the instructions were to load a new tune, turn it off then on, hit reset adaptations, and that was it. No 12 minute tune. Never had a problem.
When you do the 12 minute tune after hitting reset adaptations, you have to wait for the fan to come on, then wait 12 minutes.
For his idle problem, I suggest loading the Triumph 20219 or 20226 tune for tors/cat bypass, hitting reset adapt, then doing the 12 minute tune.If it still doesn't idle right, there's something else wrong, like maybe the tps needs to be adjusted.
The popping on decel, ie, with the throttle closed or nearly closed, is caused by a lean condition. This is controlled in the L fuel tables, which work off manifold pressure. The decel tune has fuel added at low throttle position but it doesn't work perfectly. A lot of time has been spent trying to get the L tables right. the Power Commander overrides the fuel tables. It doesn't care which tables are controlling the fuel. It adjusts the fuel under all load conditions, including hard decel, at least if you tune it on a dyno. Presumably the AT does the same thing.