When I create a Project Package, it only includes data (featureclasses and tables) that have been added to a map. There is much more data that, if not part of the map, does not get packaged into the project file for sharing. I can see that behavior with a Map Package. In that case you would expect the package to just contain the data needed to share just that map.
However, when I package the entire project, I would want a checkbox option to include ALL data (even if that data is not used in a map) so that I can share that with a co-worker and be sure they are able to have access to all the data I did.