Without meaning to cause offence, I think some nations are a little bit precious about our defence choices.
The communication coming from Ministry of Foreign Affairs (MoFA), not Ministry of Defense (MinDef). The way I see how Indonesia put concern, if the concern more on what Australia choice of defense, it will be more likely something will come out from Ministry of Defense. So far, MinDef doesn't talk anything on this matter, perhaps they want to maintain level of co-op and communication on defense with Australia.
The communication from MoFA in my opinion more consist of two thing:
1. Concern that Australia move can create SSN race in region (like I put in my previous post especially from ROK and Japan),
2. How this means for regional commitment on not using nuclear for defense.
Indonesian MoFA more concerned that this move can open Nuclear Pandora box in Asia Pacific. The way I see it, it's not being directed to Australia alone, but also to US. What's this means from US perspective, is it mean US ok with Asian developing nuclear capabilities ? If US give Australia nuclear reactor for SSN operation, will it then mean they will not complaint if someone else in the region work with (say French) to build SSN?
But more importantly this is a question to Australian stances on developing Nuclear power. Is this means future Australian SSN will only powered by nuclear, or later on it's open to operate nuclear weapons from US or UK ? What Australia stances if the neighborhood developing nuclear power capabilities ?
Nuclear is always sensitive issue, I remember back in 90's there's concern in Australia when Soeharto told Habibie to study on building Nuclear Power Reactors for electricity. The concern officially talking on safety on nuclear reactor within Indonesia earthquake prone region. However some Australia media already talk that by moving to that direction, Indonesia will develop it's own fuel enrichment capabilities (which with only few tweaks can be developed to the "next" level).
The talking in Indonesia now on potential choosing molten salt technology, also influence to satisfied regional and domestic concern on of fuel enrichment and radiation safety, as Molten Salt technology is harder to turn into "next" level of fuel enrichment and have better radiation safety.
was Indonesia I’d be far more concerned about what is happening to their north, not south.
Well that's part of concern. With US allowing Australia to have SSN, will this means the two US major allies in North of Indonesia (Japan and ROK), open to develop their own SSN ? Their nuclear Industry already advance enough, that if India and Brazil already able to build compact reactor for Submarine, Japan and ROK will able to do it too.
For Indonesia that control some major sea Lanes in the region, off course it is a concern. Instead before only need to watch US, Russia, PRC SSN. Later on can also means Australian, Indian, Japanese and ROK SSN.
Will this means Indonesia later on also building SSN ? As I have put in my previous post, not in short time. It will take much more budget and massive undertaking on Indonesian Nuclear Industry to do that, and I don't see it in near future.
Again, I don't see our MinDef concerned much, but with MoFA that make statement, it's more shown Indonesia concern for the regional in near future.
Add:
My previous post on communication more directed not on Australian choice of weapons. However more on Australian choice to use nuclear power. Again the problem that concern Indonesian MoFA is not what Australia choices of weapons, but more on potential opening nuclear Pandora box in the region.