My original itinerary had a stopover, but that was to break up the forced overnight in CGK and just because I have never been to Jakarta.
But with the cancellation of the route I was happy to alleviate the need for a stopover and just go through to BKK (in my case with CX).
On my dates, introducing the stopover in CGK also maintained the ticket at its low price - the CGK to BKK flights the morning following my CGK arrival had price premium on them, going onto BKK the next day kept the price sensible.
Having reread the EC261 wording it only states that the obligation is to reroute you to your destination (singular) and makes no reference to stopovers or intermediate routing as far as I can see.
If you absolutely have to get to Jakarta but want to maintain the value of your flight to Bangkok as silly as it is, it might be that you have to consider booking flights from Bangkok to Jakarta separately and trying to do a claim from the airline for the additional cost - but there could be many reasons that this would not work for you not least your time and inconvenience, but taking advice from a EC261 claims specialist might be worthwhile first to get their view on the stopover situation and if that is likely to work. Also bear in mind that the GA legal entity in the UK may be closed down in Autumn if they have no intention to fly here for a while so you might be forced to do the claim in the Netherlands.
A difficult one.
I had other Indonesian friends who travel frequently in business on GA, were not on an especially cheap booking, and were impacted by the schedule change, their destination was CGK. They seemed to be unable to argue that the time change to use the flights via AMS meant these flights were useless to them and they needed to be rerouted with SQ MH or CX, but that could be done and ended up having to take the refund and rebook with SQ - but I don't think there was a significant cost difference in the end. It does seem that there is a limited amount of flexibility that GA offer and beyond that there is no hope...
Good luck