I assume you're referring to the JBL Nav system, and I am pretty confinent there will be no programmers changing that as getting the access to the source code would be extremely difficult with a limited payback.
I just bought a 2012 LE with Entune and have to say that it's 10 times that JBL Nav system. I played around with the JBL system a lot at the dealers and hated it. The Entune system is not as nice as a the top-of-the-line Kenwoods, but it's still pretty slick. Wireless bluetooth music streaming is awesome, just picks up automatically where you left off. It reminds me of the first gen iPhone, there is a TON of possibilities just waiting for Toyota to (hopefully) release them. For example, you know all those Customizeable features in the back of your manual? In my Entune manual it shows all of those being turned on and off through the touch screen under setup. No more trip to the dealer!
I know a lot of people complain about the sound quality of the JBL system, personally I thought it was pretty decent (not incredible, but decent), unfortunately the standard system that comes with the Entune, is pretty crappy. It's hollow and lacking in sound definition.
In case anyone reading this thread is in the market for a new T4R, I highly recommend the Entune for function, but not sound quality... a speaker upgrade will be coming.