Hello Thomas,
Point coordinates in bundler.out files are stored in the world coordinate system. It is different from the camera coordinate system (actually each camera in the scene has its own camera coordinate system, which is oriented according to the camera orientation).
Presence of positive Z coordinates of points in bundler.out doesn't violate the statement in the Bundler documentation you are referring to, as the points are stored in the world coordinate system. After transforming point coordinates to the camera coordinate system (as described in the Bundler User's Manual), Z coordinate should become negative (for points that are visible by the camera).
At the same time, neither format makes any specification on the world coordinate system orientation. Orientation of the world coordinate system can not be determined from the photos alone, and requires additional information such as ground control measurements. Thus, initial orientation of the reconstructed model produced by PhotoScan is completely arbitrary (i.e. undefined), and can be later assigned using Ground Control dialog.