@Gradient: For this purpose you might want to use the alpha-mask, which is saved in the temp-folder (if not disabled).
Or you just use one single black surface shader to have this mask.
Anyhow, for postprocessing you did use masks (as long as I remember TG0.9 did not save alpha) so I do not see any drawback for this point.
@3DGuy: As I already wrote, turning off the clouds does not change the look and feel of the surfaces (except for the shadows, okay). In TG0.9 it was a major difference for the colours when using clouds or not, changing and twisting the atmospheres, etc.
So as mentioned above, I do not see a drawback in this point, as TG2TP gives you masks or is easy in making some. So the only advantage of turning off the sky would be rendertime (so crop it) in preview.
Regards,
Volker Harun