I have this same engine in my GS and if it is cold, it has a very brief momentary clatter on startup, but it is so short, it is almost unaudible.
You sound like you have a legitimate gripe. My guess is that you've got a valve sticking - I've been told this engine has solid lifters so there is no hydrualic lifter to "pump up." Does the engine tend to labor slightly and feel like it is misfiring until the noise goes away? This would be consistent with a sticking valve. It hangs up momentarily and "slaps" the cam rather than smoothly following the cam lobe.
Reaming the valve guides is not a big repair and unless you're just looking for an excuse to lemon, I would think you could find a dealer willing to take care of this for you. Have you tired another dealer? I'd leave the car overnight and have a mechanic and a service advisor with you the next morning during startup. Maybe bring a tape recorder. Get them to commit in writing that what you're experiencing is "normal". This is probably not something that is formally spec'd.
A shade-tree repair is to do a triple does of fuel system cleaner and use some kind of oil additive for a few hundred miles. The one mostly widely used is "Marvel Mystery Oil". It really does work in some cases. But if the car is brand new, then valve deposits are not likely the problem.
If you are going lemon, keep careful track of everything and make sure you are following the lemon law to the letter. Many people think they can just lemon a car when it generally is a pain, but the law is very specific about what has to occur before it kicks in. Once you meet the letter of the law, dealers (and Lexus) will generally bend over backwards to avoid the buyback, including getting you into another car with no money out of pocket.
- Mark