HP Tuners is just a software package that can be used to tune the engine and transmission. There are several good tuning software packages on the market.
I think you are better served to find a good tuner and let them use whatever software they are most experienced and comfortable with. There are several good companies in Florida that can perform a tune on your car. A good tune will give you a small boost in engine power and can provide a substantial improvement in how the A6 shifts. Especially if you can find a someone that can copy the "LT" transmission settings to your car.
There are numerous threads in the forum that give before and after dyno numbers for the LFX tune. Here is one of many threads about transferring the transmission settings:
http://www.camaro5.com/forums/showthread.php?t=340877
I encourage you to take some time to read through the tuning threads in the forum. It will help you understand the process better. It will help you know good questions to ask when you look for a tuner if you decide to go that route.
Good luck!