From what I understood every 5000 miles is considered a maintenance period. The message is first maintenance required soon and then it becomes maintenance required.
Make sure to have your head unit software updated as well. The Entune update and the software update are actually two different updates. The dealer will usually do the software update for free.
There is a software update for the head unit that may fix that. It is very easy to do but getting the file on your own to do the update is the hard part. Most dealers will do it for free. It is literally a 10 minute or less job.
Things are going to get sticky. I would stay away from doing it. However, there are products out there that you can use that will be much better for the job.
From what I read, the OEM Panasonic batteries cannot be replaced with another Panasonic battery because they aren't available in North America. They only arrive with the vehicle originally and then afterwards the dealership uses a different brand battery that is rebranded by Toyota.
It really depends on the warranty being offered. What does the warranty being offered to you cover and what does it cost. It may be worth it for you it may not.
Are you asking about that pebbled finish on the surface of the bottom edge below the doors? The first time I saw that I thought it was rust causing the paint to bubble but it definitely is not that. I actually don't know why it is like that.
The best advice I can give you is that I bought a 2WD model and kick myself for doing it. Having the 4WD ability is really nice even if you don't go offroad. In the case of the Limited trim model the 4WD is full time. It also turns out that the SR5 Premium model has full time 4WD as well.