I am really sick of seeing cars on a manufactures web page that don't really seem to be available. Either really sell them, or just don't even offer them.
They sell every car they show on the website. The problem you are running into is that you want cars equipped in such a way that your ideal car would not be given a second look by 95% of the buying public and so they are not regularly stocked by dealers.
You will run into this issue with any car when you want one that is atypically equipped. For instance, I had to custom order my Corolla because they just don't make Corollas with all the options sans leather to ship out and sit on lots. The reason for that is because the average Corolla buyer won't spend 20k on a Corolla and it would sit there forever if dealer just ordered them that way.
The same goes for the Lexus you looked at, your typical Lexus buyer hasn't driven a stick in probably 20 years if ever. They wouldn't entertain the idea of buying one no matter what you tried to do to sell it. Dealers see cars that they can't sell as a liability and since manual transmission Lexus cars don't sell, you just won't find one sitting around.
Certain cars are more like niche vehicles and come typically equipped with manual transmissions and other hard to find options on other cars (or at least more typically equipped with these options than other cars) BMW 3 series and Miatas are examples that come to mind. Before the Mazda had the Sport AT, it was almost impossible to find an automatic Miata.
If you need a car now and won't drive automatic, then you should consider looking at Audi, BMW and Infiniti. I frequently see Audi A4, BMW 330i and G35 Sedans with MT on local dealer lots. There aren't many, but there are more of them than there are on Lexus dealer lots. If you really want the IS250 with the manual transmission, don't really care about color and other options and you can wait, ask the dealer to do a nationwide search for one and acquire it if one is available. If one isn't, custom order the car. You'll have to wait 3-4 months for it, but you can get exactly what you want.
Honestly, I'd order the IS before buying an all new BMW. Do you want to be R&D for BMW, finding all the manufacturing and engineering issues in your new car and then waiting for them to come up with fixes?
Simply wanting a manual transmission isn't really that small of a small market. I realize that most people want a automatic, but their are still plenty of manual drivers. Most of my friends are too and we are getting old enough to be looking outside of the Japanese boy toy market. If Toyota/Lexus wants to sit by and presume what buyers really want, then they can do that. They will be missing out on a large enough part of the market.
As far as being BMWs R&D, the current 3 series is not that new and I'd wait for a 08 at this point anyway. Also, they have full 4 year 50K coverage. They will replace any worn part on the car except tires. That includes brake disk, pads, shocks, ANYTHING. Oil changes too. That is really the only reason we are looking at one. Lots of people can afford the price tag of a car that cost more, but not the maintenance.
I'm not too big of a Audi fan. As far as German cars go, I really only like BMW and Porsche. To me a Audi is just a over priced VW and they can still have the same quality problems. I will never buy another Nissan product in my life, so that is out of the question.
Too bad Toyota gave up, lost it's performance market. Cause they might have had some boy toy cars in the past, but they were quality boy toys that lasted a long time.