This was Toyota's explanation for the rough idle issue:
The two automakers diverge on the remedy, however. After 100 miles of learning the powertrain and the driver's driving style,
AN reports that the ECU's mapping is pretty much baked in. If engine operation exceeds the established parameters, at low revs the engine succumbs to uneven idling and stalling as the ECU tries to recalibrate
to a new range of tolerances. Toyota has said that if the issue is suffered by a car with less than 100 miles, the ECU should be reflashed, but that cars with more than 100 miles should have their ECUs replaced. Subaru, though, has said that the ECU doesn't need to be replaced no matter the mileage – a reflash is all that's required. It appears that some owners who have had the reflash have suffered the problem again.