Hi,
The kit is specifically tuned to handle high power applications, such as a TRD supercharger. They actually say it is for a TRD-supercharged vehicle. What I can tell you is that it works. It really makes the shift very fast and instant, and makes the transmission able to handle much more power, up to twice the power of the standard transmission.
I'm not sure how different is it from when you send your valve body in; what I think is that when you send your valve body in, they will upgrade it for you depending on how you want it. For example, if you do drag races, they will upgrade it to give you maximum acceleration, but will compromise on comfort. If you want it smoother and more comfortable then they will do it for that.
I believe if you ask them to upgrade it for more power but smooth operation, like with a TRD or URD supercharger installed, they will just install the kit they sell. The rest of the money is for labor and core exchange.
In my opinion, the difficult part is removal of the valve body. Installing the kit is easy and fun, albeit quite messy. If you are afraid of messing up, have them do it for you.