There is nothing to support the flight passing over Indonesian territory, yet there is strong evidence (Indonesian statements) to the contrary.
I'm playing devil's advocate here - what if the Indonesians aren't telling the whole truth? Governments in that part of the world are a little touchy about national security and air defence. Would the Indonesians admit to the world that an unidentified aircraft flew over their territory undetected?
You seem to have unswerving faith in the Indonesian statements, yet discredit the information released by the Malaysians as a 'smokescreen'.