PI 3, Pi 2 and noise
As some of you have found, the Pi 3 emits a small tone that is quite annoying and unacceptable. The Pi 2 does not have this tone, but it has some noise that occurs as the Pi 2 is accessing the SD card and other peripherals. As mentioned before, this is coming into the 503HTA via the 5V rail. While we do have a filter there , it is primarily for high frequency EMI (above 1Mhz), so does nothing for audio band noise.
A proposed solution is to remove (or bend out of the way) the two pins from the Pi GPIO header that is used to feed 5V to the Pi. This would then require the Pi to be powered via it's micro-USB power connector as usual. The good news is that doing this removes the noise completely, including the Pi 3 tone. This tells us also that it was not the WiFi or Bluetooth causing this noise. Note that we did not try to create a lot of traffic via WiFi to see if it causes noise under other circumstances.
The bad news is that you have to modify your Pi, which is something not everyone will be comfortable with. For Pi 2 users, it is probable that you could find the right setting of headphone output resistance that reduces the noise to acceptable levels (as seems to be the case now). For Pi 3 users, it is the only practical way to use the 503HTA with the Pi 3.
Below are a few photos of what we did to the Pi 2 to test (Pi 3 is the same).