Hilarious that people keep posting asking for a solution when the solution has already been posted. Buy a USB Bluetooth dongle. The problem isn't the antenna nor the software stack. The same software stack is used for external BT devices. The problem is the built in bluetooth uses a very limited UART interface and it lacks DMA and the bandwidth to support high quality streamed audio. Can't fix that with software.
I've been chasing down the same problem--very difficult to trace the problems, but it doesn't seem to be anything wrong in Kodi, it's actually in the bluetooth stack. With a bluetooth keyboard connected, I found when the Dolby Digital audio started to cause problems it also caused the keyboard not to work.
In trying to troubleshoot, I found other references to problems with the built-in bluetooth device on the Pi3. Since I happened to have a Bluetooth USB dongle, I disabled the built-in bluetooth by adding the following to /flash/config.txt
This disabled the built-in bluetooth, but does not disable USB bluetooth. Interestingly the built-in bluetooth is not USB, and I believe the root issue is actually the bandwidth for the data interface with the built-in bluetooth being insufficient for hi definition audio.
Anyway, with USB bluetooth device streaming audio works perfectly even with Dolby Digital. Seems annoying to have such a limitation on the built-in hardware.