Can you give an example of a type of project which would theoetically have different gender distributions of contributors than other projects? That doesn't seem obvious to me.
Have no idea. But also have an inkling that distributions would differ (and not necessarily the way you'd expect) in projects that require a specialized skill set, such as e.g. top notch design skills or knowledge of DB internals and such.
The point being, as stated the whole thing very much resembles the Berkeley gender discrimination study, so proposed improvements are quite obvious: break things down further by project, see if you can glean something from per-project (or at least per-domain) distribution. There might be nothing there, mind you, and the stated conclusions might still hold, but without controlling for the confounding factor there's no way to tell, and the conclusion of this study is therefore not above suspicion.