I suspect that you're asking a great deal for perfect dialogue from Jakarta Radar Control
yes but I fly as well, and when in IFR ( or VFR in controlled airsace ) if I request a descend and I hear back : " copied " I am never going to start decending , and would ask again if we are cleared to descend. Anywhere on the globe. Therefore I think the full exact R/T exchange would be helping us understand why ( and if) they did take this " copy" as an ATC instruction .
If he did say 6000ft then the crew probably thought (wrongly) they were OK
Normally not the kind of assumption a 57 years old test pilot with over 10.000 h would do. In this situation (outside radar vectoring) The ATC clearance / responsibilty is only with regard to separation with other traffic, not with terrain.
A guy like this would know that for sure.
The clue(s) are somewhere else I would say.