Not so crude, it all based upon calculation and IAEA spies/employees/observers in these reactors.
How raw material (the uranium pebbles are obtained) is procured I don't think Indonesia has it own enrichment facilities (specialized facilities where raw uranium is process and higher end uranium is obtained) so it must be imported. if it is imported they know the exact specifications how much is which isotope and for how long it will be used.
I don't think a research reactor can produce weapons grade Plutonium. Lower grade yes but weapons grade is a huge challenge.
Everything is recorded, any discrepancy IAEA raises alarm.
Simple answer no, as long as the reactor is under IAEA nothing could be done. A country can follow Pakistan's example first develop knowledge base a wide one, train young one in Nuclear Physics. We have or had three types of hiring the brilliant ones right out of college ( I was one of those who was offered) my teacher himself was brilliant physicist, two student apply for a specialized nuclear physics graduation course in IAEA controlled reactors, three send the brilliant ones from the graduation program to international research facilities. They bring back more expertise.
Once a country has sufficient Human Capital then it starts a Nuclear program which is not on the radar (I am writing it causally but the way we did it, it is a PhD course worth of expertise/subterfuge and sacrifices). One a country develop uranium enrichment expertise to weapons grade then cold tests, a suitable casing/triggers and finally "The Test"
In tandem a country must develop suitable delivery platforms, a.k.a. missiles and lots and lots of them.
It is a monumental task, very few Islamic countries are up to the challenge it has many many dimensions. Its not just about the capability its a huge undertaking.
We have both type of facilities those where we allow IAEA and those where we don't allow IAEA.
Besides now we are a certified Nuclear power, whether we get included in the exclusive club or not we are what we have made ourselves.
At the end of the day its a deterrent not a weapon meant to be used.
