>[W]e should be able to assume that they obey the physical laws of the universe
I don't think anyone is assuming otherwise... all I see is statistics and sampling being argued. You'll have to endure my wall of text, though, sorry XD.
Let's take the planets again. We don't know the size of every single planet in the galaxy (i.e. the planet size histogram), so we need to make a guess. So we've been using Kepler's exoplanet observations, knowledge of planetary geology, etc. to fit a model, and it's well developed (http://exoplanetsdigest.com/2014/07/25/exoplanet-statistics-...). The size distribution is quite well understood, its bounds and modes are well defined. It's unlikely that our best guess of what the average size of exoplanets is will change drastically the more we know about planets. That is why the article's first conclusion is legitimate.
Now back to (sentient) species, and my original point. The definition of life in the SETI context has to be VERY wide. It has to encompass any scenario for a species that we might consider "intelligent" -- and not just little green men. It might have (some would say, inevitably) evolved beyond the biological, and still be considered sentient. After all, life on Earth has only existed for ~4By, compared to ~13By for the Milky Way. As a base for extrapolation, just think how different to humans extreme life on Earth is. (http://www.livescience.com/13377-extremophiles-world-weirdes...) In any case, there are bound to be some weird-as-shit species out there, whose composition still obeys the laws of physics. In other words, there is almost certainly many statistical modes of life out there that are, or can become, sentient.
With that in mind, there's a very good chance that the overall size distribution of (sentient) species does not match the one the author used (that of vertebrates only). In statistics-ese: if the distribution is multimodal, the average of our unimodal sample is not a good guess as to what the true average really is.
Maybe we can agree upon that?