RJ posted this thread regarding the changes to the v2 MR 16.
The updated controller information is here http://diylightanimation.com/index.php?topic=3175.msg32205
It is not limited to only 12 volt input. As stated in RJs post it can run on 7 to 24 volts. I'd go with the original designers take on this.
I have a lot of 5v devices in my display and I had a lot of the same questions. In short the best way to use the MR16 is to have all the devices that are being controlled use the same voltage (7 to 24v) as the input power supply. In my case I found it better to control my 5v devices with a DC SSR running off of my Freestyle controller. To be clear RJ does not have a DC SSR design but they are out there in some of the other forums. I think it has been suggested or asked if he may come up with a DC SSR design but I don't know his thoughts on that.
I have some of this v2 board but I will be building them as low current constant current controllers to run LEDs.
Just another opinion.
Alan T