I hate to admit that the dealer may know what they are talking about, but my 2006 400h makes a rattling noise at idle too (more noticeable when first started I believe). I can't really make out the noise in your youtube video, but it must be what I am hearing.
Anyway, why do I think this? There is a TSB about resetting the ISC (idle speed control) and one of the things it mentions is that 'transmission gear clatter noise at idle is more pronounced'.
Regardless, if you have ever disconnected or run your battery below 7 volts (the auxillary battery, not the traction battery), you NEED to perform the ISC learning procedure. You can ask the dealership to do it, but it CAN be done without having to hook the vehicle up to the Lexus specific diagnostic computer. I've posted instructions at
www.lexusownersclub.com in the hybrid forum. Do a search for "ISC learning". My mileage went from around 10l/100km to 8l/100km and I was able to drive further on battery only.
Here is a page from the TSB that refers to the rattling noise..again, the TSB makes the procedure look complicated, but it can be done by an ordinary mortal