True, its not exclusively a problem in vehicles with poor maintenance records, but not changing the oil on time exascerbates the issue, the fact that the engine doesn't drain fully (a lot of engines from a lot of manufacturers dont) I'm just saying, get the engine flushed, use synthetic oil, change it every 3 k and use a good Lexus filter, you're going to save yourself a lot of headaches and trouble. Much less likely to have an issue. I would agree with the dealer's assessment that probably the gelling in a car as young as yours has at least in part something to do with the frequency of oil changes. Regardless, the car is covered for 8 years so whats the big deal?
And if the engine requires replacement (which can be the case with the gelling if its bad enough) its gonna cost you more than 5k, probably closer to 10 or 15. A transmission on these things is around 8k.
As for the $40 and $90, while I'm the first to say Lexus dealers charge prices that are beyond excessive and extreme for most if not all services and parts (they markup parts as much as 300%, see Steviej's turn signal bulbs. $10 each at Lexus, $3 each at Toyota for the exact same bulb, dealer charges $80 for a CD magazine when www.lexus-parts.com sells it for $30 and still makes a profit in there somewhere, Lexus charges $120 an hour for labor, Toyota $60 when the training and certification is the same) however, if the customer will pay $40 for a light bulb, or $97 for wiper blades, then thats business. 95% of Lexus owners I know expect these costs, are happy with them, and even get suspicious when they're lower.
Its just the chosen few of us that know better.