Well, I have just tried it out, and got even more confused. So the documentation states that it will ignore any custom voice commands. I was under the impression that means all the custom intents, and sentences. But this is not what is actually happening.
If it transcribes a sentence that is recognized by your intent manager then the intent will get recognized and it works as it always does.
If it transcibes something that is not recognized, than it will simply not recognize any intent. It works similar to the text input for me. If I type anything that my sentences do not reflect, i simply get an “error” message.