The problem is that Indonesia doesn’t recognize dual citizenship, so obtaining an Indonesian passport may require revocation of all other citizenships. And it appears he used it to travel internationally. He was 19 or 20 when he made the trip, IIRC. Thus, if he did travel on the Indonesian passport, it's likely it was issued before he was 18, which would mean any revocations would be ineffective.
I don't think that's true. Using the passport is a significant act re citizenship.