I'd just like to post my agreement to your assesment in the bird's eye view. However, there are a few discrepancies with the credit, regarding option 2 for naturally ventilated (or window ventilated) facilities.
1) The credit language does not require a 30% increase for this path. It requires the minimum airflow rates from section 6 of ASHRAE 62.1 to be predicted by the simulation for 90% of the occupiable spaces. This in itself is contradictory to the standard in as much as that the standard only requires section 6 for mechanically ventilated spaces...but let us have LEED pick and choose what it wants. That being said, when a window is closed the air flow is next to zero, and when it is open it could be as high as 40 ACH. So even those picked minimums can be met if you assume they mean the daily average (which would make sence from a indoor air quality point).

2) The part that makes this credit VERY hard to achieve with option 2 for naturally ventilated buildings is that you have to predict a reasonable user comfort is maintained (it's actually the intent of the credit to increase user comfort). How comfortable is a user when he opens a window in winter for some fresh air? How comfortable is he when he leaves the window closed because it's freezing outside and stuffy inside?

Although, there are no set criteria to the required comfort levels in this credit, there are many acceptable comfort criteria that can be tested and applied to this credit and help prove adiquate comfort levels. ASHRAE 55 has comfort levels defined for thermal, draft, and even addresses CO2 levels. European Concerted Action Report No. 11. Guidelines for Ventilation Requirements in Buildings, 1992, fig. 3 shows a comfort level related to CO2 as an indicator for indoor air quality.

All of these factors can be modeled with the right software and the right know-how, though due to the short timing of window opening and closing events, you need a pretty detailed, short time-stepped model.

Goodluck to all who try this option, and write me if you need some pointers...it can be done (properly) even 99% compliant to ASHRAE 90.1 and if you imploy the exact window ventilation on both baseline and designcase models you don't even need an exceptional calculation method.

Jean