The engine noise can still be conducted through the body of the plane. With the kind of ramjet being talked about, I think that's still likely to be significant even at very high altitude.

This effect would help mitigate the noise heard by people outside of the plane (but I suspect that noise is negligible compared to the sonic boom), but in the plane the sound would mostly be propagated though the fuselage of the plane, not through air, so it's not going to help.