Between the official account given by the PKI and the various alternatives postulated by scholars like Benedict Anderson, do historians know what really happened?
Not really, however there is new evidence found in Beijing which is as follows.
Recent research, astonishingly in Beijing, is starting to shine some light into this dark corner of history. In 2008 the Chinese Foreign Ministry opened its diplomatic archives covering the years 1961 to 1965.
Before they suddenly closed in mid-2013, Taomo Zhou discovered a document that narrows down this historical detective story. On 5 August, 1965, the PKI general secretary, Dipa Nusantara Aidit, was in Beijing and led a small party delegation into a meeting with Chairman Mao Zedong and other top Chinese figures.
After hearing a report on Sukarno’s health, Mao got straight to the point. “I think the Indonesian right wing is determined to seize power. Are you determined too?” he asked Aidit.
I doubt that Indonesian government is willing to open up about it seeing what happened to the last president who apologised about that, but this isn't relevant to AskHistorian.
Source: http://asiapacific.anu.edu.au/newmandala/2015/09/30/mystery-of-indonesias-coup-continues/