Yes, Highlander still has an inside fuel door release. You might get an argument both ways about how good of a feature that is. (Better for securing access to the fuel filler, but a problem when it freezes in the cold or malfunctions and you can't get the door open.) So removing it isn't necessarily de-contenting to some people. I used to think that the remote door release was the greatest thing in the world and I was disappointed any time a new car didn't have it. Then I was caught out in freezing rain one night and the fuel door on my Highlander froze up. I had to drive home and carefully thaw it out with a hair dryer before going back to the gas station. If I wasn't close to home, that might have been a real problem. Now I see both sides of the debate on this one.
Toyota transmissions haven't had a dipstick in a long time. They're supposed to be less maintenance than transmissions made in the past. That doesn't mean you can't service the transmission, but it's a bigger hassle than it should be. I'll agree with you on that one.
I think many Toyota products have some amount of soundproofing. Of course, the more you pay, the more you get. That's one of the reasons you pay huge dollars for a Lexus - it has more soundproofing material than its Toyota counterparts. Highlander has quite a bit of soundproofing, especially the upper trim levels. I remember when cars had no such thing as soundproofing. So I wouldn't consider that de-contenting either, but there is clearly a link between price of the car and how hard they try to make it quieter inside. It also depends on the model, and whether the target audience for that model considers quiet to be a feature. My Tacoma seems a lot louder inside than my Highlander, but if you ask most Tacoma owners where to spend the dollars, quiet won't be high on the list with the preference there going to off-road capability.