When I applied for a single entry visa to Indonesia, the Indonesian embassy in my country approved it within a week. However, when I went to apply for a multiple entry visa, it took about 3 times as long because they said that they have to send all the details to the Interior Ministry in Jakarta and get their approval. I'm curious as to why that is the case. What do they check for? Is this a common practice?
Generally, long term visas and multi-entry visas do receive greater scrutiny, as the country would need to assess not only your trustworthiness for one trip but also the future ones. A multi-entry visa also requires additional justification.
In particular, I believe in general Indonesia requires a specific purpose and an Indonesian sponsor for multi-entry visas, which is an additional check that needs to be performed. The checking of sponsors can be better done in Indonesia than by representations abroad.