Well, if you ask me I'll tell you to fly from KUL as thats where I'm more familiar with.

But I think SIN has better connection to Europe, while KUL has better connection to Indonesia (if you consider Airasia (AK)). Do bear in mind AK's terminal is in another end of the runway away from all airlines (LCCT - low cost carrier terminal). Their tickets are cheap, probably same price as your ZED or a few dollars more but if you can bear the pain of hauling your bags from 1 terminal to another (the rickety bus ride cost you 1 EUR and takes about 10 min from 1 end to another) , Taking it is one of the best option as they are frequent and flies to many indonesia destination.

I know KL flys KUL-CGK but not frequent. No one takes it, so they sell super cheap and as a result, quite full at times.

MH has plenty of flights to CGK, so does AK. Question is which Indonesia destination you want to go? I wouldn't recommend Indonesia internal budget airline considering their safety record.

Europe via LHR or FRA should be ok as you'll have BA and LH options on top of MH

Yes, the standby procedures mentioned above are correct. I normally hold spares so that I can be listed on multiple airlines. BUT if you are really nice and talk to them nicely, they would give you an indication whether you'll have a chance and if you should stay listed. I was in NRT and listed on a pretty full CX and I wanted to pull my ticket out to go to NH (which is in another terminal), but just as I was about to pull it out, the lady told me that the situation has changed and now I'm quite high chance and I should stay listed. And having said that, in Asia, if you know the right people, your odds can be pretty high