While they are transparent the events happened, they are not transparent about which packages and what authors are being flagged, which is unfortunate.
Considering they are admitting they will always obey government commands, including regarding non-disclosure of actions to affected users, it is prudent to assume they are, in fact, not transparent about events; only about those events which the government has let them tell you about. Other events (e.g. National Security Letters) may or may not have occurred.