1. All manufacturers, luxury or not must meed CAFE standards. If you look at the RX 300 EPA estimated gas mileage goes from 20 in 1999 to 26 for the 2004 models. So even the big boys have to do something to make their fleet average mileage meet CAFE.
2. RX 300 is an SUV with a tall profile, and a CD higher than a sedan. Part of the mieage problem is going to be wind drag at speeds above 55 MPH. However, your 20 MPG is much better than a comparable SUV from the late 1980's, which were lucky to get 16-18 MPG highway average.
3. You can holler all you want about dirt in the engine, but all other things being equal, a more deeply pleated and layered aftermarket filter will allow better air flow and clean just as well for a longer time period than a stock filter of the same porosity, but less layers and less overall area.
4. Oil on the MAF is moot. If the filter is cleaned and oiled properly, that's just not gonna happen.
5. You have EGR, an air pump, a catalytic converter system, an ECU that tries to keep emissions low, and more that all works in conjunction to keep emissions down. Even with an aftermarket intake, you still hook up the EGR reabreather hose and the gas tank vapor canister hose, so there's no chages made to emissions controls.
6. VVT? Why did they come up with that? It's so the engine can run with low emissions at normal loads, but still give some increase in performance whan you mash down on the throttle, that's all.
7. If the engineers didn't have to worry about any of the above and wished to sacrifice a little smoothness, they'd be pumping out 3 liter engines with 300 HP, and that would be more "optimized" performance, right off the assembly line and into a showroom near you.