Upvote:2
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.