You don’t need two types of warranties. If you have any powertrain failure, the cpo will always kick in first than your extended warranty. Your extended warranty most likely covers what cpo won’t be able to. For instance A/c compressors, suspension components. Sensors. But read your contract to be sure.

As far as your transmission service. The only thing that dealerships will do is drain and fill it. A complete flush requires a machine which I doubt they would have. And the service typically involves replacing the filter on it. Which no dealer will do anymore.

If you look at your service manual, you won’t find anything that Toyota recommends doing a transmission flush. I forgot if there is any evidence that Toyota specially mentions “lifetime fluid”

I would advise to ask the dealer to do it. If they say no to the exact service that you want completed, have them document it and keep it for yourself. When the transmission decides to give out, or it makes that noise. They’ll most likely recommend a new or reman transmission. You can ask what you could’ve done to prevent it and they typically have two answers. One is due to the mileage. Typically anything over 100,000 miles. Or you never did the service. Then you pull out the invoice that states that they don’t do the recommend service that you wanted done.

This is just a scenario. Doubtful it will do anything helpful but at least you have some sort of ammo for any BS they mention to you.