I've installed free-air subs in the Lexuses before and they sound awesome, usually better than putting huge boxes in the trunk. The problem is people don't know what they are doing, and most companies make low end free-air subs that suck, rather than high end ones. We actually did a lot of replacing back yard/Best Buy installed boom boxes with free-air setup at the shop I worked at. I recommend the SoundStream Exact subs for free air, because they are one of the best subs on the market, and they happen to work free-air as well. They are made for sound quality, but will handle a good amount of power.
Free-air setups are great because they take up almost no trunk space, add little weight to the car, and play very linearly. But most installers don't take the time to do it right. Think of the trunk as your box, make sure to minimize the excess leaks, especially the ones between the cabin and the trunk. Use dynamat, or some other brand's product, over the entire rear deck, and also on the underside over the seam between your wooden baffle and the rear deck, as a membrane to seal the air leaks. DO NOT CUT OUT EVERY SINGLE HOLE IN THE SHEET METAL OUT OF THE DYNAMAT, THIS DEFEATS THE PURPOSE, ONLY CUT WHAT IS NECESSARY. If your installer does this, take it as a sign that he has no clue. This goes for where ever you use Dynamat/sound-deadening throughout the car.