I think this is a limitation, imposed for security reasons and restricted at the OS level.
Let's analyze the security threat, first of all. If you were able to play custom audio files to the callee, a whole world of cons opens up: you could trick customer supports, you could pretend to be someone else, you could give unauthorized purchase confirmations, and so on. For this reason, neither Android nor iOS allows this functionality.
On Android, you won't be able to do so in a programmatic way, simply because the current APIs won't allow you to do so. It is stated in the official documentation as well, as pointed out here. If you dig into the source code, you can probably enable this feature by accessing the microphone output during a phone call, but that would require running your custom version of Android. A good starting point would be the AudioTrack
source, available here.
EDIT: a good example of an audio mod involves enabling the Nexus 5 earpiece as a second loudspeaker (requires root). Can be found here.