Planet mass is usually a parameter that we have, even though it does not influence the position of the habitable zone (so Mars is out).
The simplest calculation does not involve an atmosphere and just looks at radiative balance from black body radiation and is probably the kind of calculation they're talking about in the article. For getting the real temperature many parameters play a role and most are not available, so they just use a first guess for the habitable zone.
An atmosphere will change this radiation balance, with absorptive gases and aerosols blocking radiation (both in- and outgoing) and by distributing the heat more evenly. Atmospheres can be detected if the planet's orbit is good, and it is possible to get an idea about the composition (mainly water, methane and CO2 so far), as well as see changes which are probably due to weather. The method used is to look at the center star's light that travelled through the atmosphere of the planet when it traverses; it's also possible to look at the atmosphere's reflection when the planet is almost behind the star. I can go find some spectra if you're interested.
Another important parameter in the equations is albedo ("ability to reflect radiation"). Warmth left from the planet's creation and radioactive decay as well as gravitational effects from other bodies (eg the effect Jupiter has on it's moons) are the other possible energy sources. Geological activity of bigger planets could lead to aurora and allow detection that way, but the instrumentation is not up for that yet..
In our solar system, some moons are considered candidates for life, being covered with a thick layer of ice and possibly containing water underneath and they're not in what is considered the habitable zone of the system. The concept is more of a guideline at this point, really, and also only looks at water (arguably the best candidate for life, but not the only one).
In case you want more information about anything in particular I can find some papers or overviews.