An interesting question:
How would one modify the canonical world generation rules to cover regions which were not conveniently terraformed in the distant past?
I'd suggest the following:
Assume that all "breathable" atmospheres (codes 2-9, D, E, and F) are actually "exotic" (code A), unless a "saving throw for the presence of aerobic life" is made. The nature of these "exotic" atmospheres is likely to depend on their density. For instance, a non-terraformed planet of size code 3, with a "very thin (tainted)" atmosphere (code 2 or 3) could be very much like Mars, with an atmosphere of mostly carbon dioxide and a little water vapor. Such a planet with a freakishly thick atmosphere (code 8 or 9) might be more like Saturn's moon, Titan, with a cold, thick atmosphere of mostly methane and perhaps ammonia.
How does this sound like a workable compromise between preserving the inherent simplicity of the planet-generation rules, while adding a realistic mix of atmosphere types?