Hi, my name is John (from Sydney, Australia),
I purchased a Lexus IS300h in August 2013 and have also experienced the transmission "rough spot" in this car. I'm a retired automotive steering/suspension engineer, and drivetrain NVH (indeed any NVH) really, really annoys me!!
Yes, there is undoubtedly a drivetrain vibration problem in the IS300h when the engine is operating at low load at about 1200 - 1300 rpm, which corresponds to about 80 - 90 km/hr on an open flat freeway. It is most noticeable in ECO mode where the planetary "CVT" response is designed to be sluggish (on purpose). In Normal or Sports mode the problem is masked somewhat because the rpm advances through the 1200 - 1300 speed range - so you just get a shorter "kick" in the vibration.
As one of the other LOC bloggers say, the vibration resembles a "rumble" or interior "boom" and sounds a bit like driving a manual transmission car in top gear at excessively low revs. As an automotive engineer, my guess is that it is caused a drivetrain vibration resonance, which interacts with a fundamental frequency of the air volume in the passenger compartment. (hence the audible "boom"). I wish I had my old spectral analysis equipment, and then I could tell you the exact frequency!!
Anyway, "Mr Lexus Drivetrain Engineer in Nagoya", you have clearly missed this problem in your exhaustive testing, and there is a number of Lexus IS300h new owners in the world quite annoyed by it. The local Lexus service guys cannot do anything about it. We need an engineering fix, may be a remapping of the drivetrain ECU or changing of the transmission mount spring-rates to eliminate/attenuate the problem.