While Duterte is indeed a weird one and his policies regarding Philippines sovereignty in SCS not only doesn't make sense, but are actually endangering Phil sovereignty as a country and also the region as a whole. To claim that we, Indonesia, would rather see the Philippines become fragmented is way too far...
For one, Indonesia always believed in the territorial integrity of nation states, we never had this idea that breaking up states is a good thing, especially not to a neighboring and friendly state. A fragmented Philippines also means the smaller states will be more easily influenced (or be frightened) by China, remember they still have communist insurgency ongoing till today (NPA), so communist ideals are still alive in some segment of their society and China can make use of that or even turn them into allies. The southern Moro states would probably become fundamentalist Islamic states where radical militants will find safe haven and training grounds.. We are already having issues with these Moro based militants and it will only get worse in a fragmented Philippines with no central gov. Piracy and kidnappings will also be a major problem in the area. So no, I don't see how a fragmented Phil will be beneficial to us or to the region, most likely it will be worse. And anyway China already has military bases in the Spratly islands and the distance to us is more or less the same.
However if we are to be worried about a possible Chinese military base then it's not in the Philippines we should be worried about... but in Timor Leste. China is already investing a lot in TL, most of TL new infrastructure projects are financed by China, like the Presidential palace, Army HQ, airport, toll roads, etc. However TL economy is not looking good... Their oil and gas fields are already past peak production and are now decreasing and is estimated to run out in the not too far future. Even today TL is already using their Oil & Gas savings fund to finance their annual budget. It's not hard to imagine TL becoming broke and indebted to China and be forced to lease their ports or airports, effectively turning it into a Chinese base... With TL located in our soft underbelly such a scenario is going to be a disaster for us (and to OZ as well), China will be able to freely monitor and spy on in the area or even station their military assets there.. It will be like having a dagger pointed to our belly. Hopefully this is something that our (and Oz) gov have anticipated and are taking steps to prevent such a scenario.
