FD will get to landing on planets with atmospheres, but it will probably take some time.
What they've done with planets without atmospheres is bloody amazing already. But David Braben has talked already in livestreams about actually putting life on these planets.
Have a think about what sort of planets with atmospheres you could have:
1. Atmospheric planets with no/trivial life without (like Mars)
2. Atmospheric planets covered with non trivial flora and fauna (like Earth without people)
3. Atmospheric planets with human breathable atmospheres covered with human life
I suspect they'll do these in three stages. Firstly, the atmospheric planets without significant life. There's two major things that need to be done there.
a. Adjusting the terrain generation to account for erosion etc. Note that atmospheric planets may have water (or other liquids) so rivers etc may need to be generated (perhaps planets without water could be done first).
b. Designing appropriate weather systems and graphics. This is based on surface temperature, atmospheric composition and density etc. Given the wide range of possible atmospheres this is a lot of work in itself.
To do just the above _well_ is a heap of work. To do it not well is less work, but I think David Braben wants to do it well.
And at that point, we haven't even added flora and fauna.
Adding plant life will probably be the next step. But you need realistic generation that reflects the atmosphere, the availability of water and sunlight, which generates and appropriate amount of foliage for different parts of the planet. Perhaps we also need to consider plant life that looks quite different based on the class of star, a spectrum more towards the infrared (cold star) or ultraviolet (hot star) may produce different sorts of fauna.
You can imagine, this is a huge job to do well.
Then we've got animal life. Not only do we have to generate appropriate animal life and a food chain that looks realistic, but the stuff has to move as well! Even more difficult than the last task.
And we haven't even got to human populated planets. These will have huge cities, but in many cases surrounded by less populated wilderness.
We're talking 20-30 years to do this all well. It'll come out very piecemeal. But what I'm sure about, based on Horizons planetary surfaces, when bits do come out FD I suspect will be at the top of the game across the industry in this regard.