The doors are triple sealed, its just a very small piece of trim, no difference in noise or anything like that.
I could post a picture but I don't think you'd be able to tell, its just a very small little piece right at the bottom of the door panel....
Its all relative. I have an independent Lexus repair shop that does the 5k service (oil change & tire rotation) for $80. Its great that you have a shop that does the oil change for $27 and Discount Tire does the rotations for free. Personally I don't have the time, or the desire to take the time to take the car two places to have one service done.
The dealer is more (about $180) for that service, but it was always nice to drop the car off and get a nice loaner and be able to do all of it on my own time, or have the dealer come to my office and get the car and leave a loaner. I also had a good bit of warranty work done, and some things done for free that the dealer didn't have to do such as remove & install a radio bezel that was scratched for me, replace light bulbs for free because of my relationship with them and the valued nature of my business to the service advisor. All in all the service was great and having the car maintained was a pleasant, upscale experience that I enjoyed.
As the car got older I made a change and now enjoy saving some money, but when I buy a new one I will probably take it to the dealer again.