I noticed there is a new joycon PCB; do you have the one with multiple inputs?
With the older one(single input), the device gets its power from USB, not an external power source. The device is simply measuring resistance over a line, just like an ohm meter. If you add power into that line it will throw everything off...maybe even damaging the device as it's designed for the 5V that USB provides. Volts kill electronics, Amps kill people.
I would imagine the new one follows the same rules.
Edit: Re-read the post 2 above.
The stock radio may supply voltage and read the voltage drop, the joycon may do something similar. Regardless, no extra power need be supplied to the lines!