Now that I've been back in the car for a few days, I think it's probably fine. It's not like the 911 I had as a rental or the Boxster either, both of which were about 10 years old - those things had quite a bit of vibration at idle. It smoothed out once moving, but wowee... On the other hand, the IS 500 is just a very subtle vibration.

 

Again, people are overthinking this car. Vibrations through the shifter is completely normal. It's physically attached to the transmission. Transmissions vibrate when the car is on.

Its the same reason you shouldnt always rest your hand on the shifter when you drive. You're placing unnecessary weight and pressure on the components of the transmission.

 

The vibrations to me mean that, if anything, we should be thankful that we still have a direct mechanical connection to the transmission rather than silly push buttons or tiny electronic control sticks.