Has the notion of E or ICE or some other chemical drug come into the picture yet? HM is out of home; TS is charged by LE at the party - takes selfies while under arrest; belligerent behaviour at hotel. Escalation to violence. Then murder. IMO the young man may have carried a supply into Bali quite easily. Would also explain the erratic simplistic behaviour following the murder.
SM thought this was a new start for her and daughter - removing her from an environment/bad company. Certainly has a whiff about it, to me. If they had as much as a hint of illegal substances in their blood (and that was 100% certainly tested by LE) then they're history; lock the door and say goodnight. This is all JMO of course.
Re passports locked up by reception - that is the norm for all tourists. Is done at the time of booking in. TS room was booked/billed under SM authority (even if it was actually done by HM) so therefore his passport was locked up under her name not his.
Haven't read anything that would indicate that either of them were into drugs any stronger than pot but you never know.
While locking up passports and other valuables by tourists is considered a very good idea, this is normally done in safes provided in the room that you set with your own entry code. The St Regis does have in room safes and likely at a high end resort like that the cost would be included in the room fee. However they are usually pretty easy to break into for anyone truly inclined to do so. For extra security you do have the option of using safes at the front desk reception for a fee and for some reason this appeared to be a preferred method for SWM. I wonder why?

MOO