Natural ventilation

If the space is not conditioned in the proposed case then it does not require heating or cooling in the baseline case. The energy performance has to be achieved by comparing the proposed project as designed with the Appendix G baseline.

Sounds like you need to figure out how to get additional savings from the systems being installed. You can claim savings for natural ventilation and it would be an exceptional calculation. See Appendix D of the Advanced Energy Modeling Guide for LEED. You will need to demonstrate that the natural ventilation will deliver similar comfort conditions to a mechanically cooled space and use software that can model natural ventilation (many cannot do so). Even if you can do all of that I certainly would be highly skeptical of such a claim for a space which is not even fully enclosed. You would also have to justify any attempt to condition a space open to the outdoors.

This is IMO one of the trickiest areas in the system, i.e. conditioned areas that are open to the outdoors. Probably, it is the intent of USGBC to change industry trends for the better, so such areas should in principle seriously disadvantage the project from attaining LEED certification. Possibly, you could argue that the conditioning system serving the non-enclosed area is per say excluded from the scope of the 90.1 standard and should therefore be considered process loads on the system. In your case, you're stuck again with the problem that when almost the whole project energy is process, then you have very little "pie" left to gain efficiency advantages against the baseline. And prooving a process baseline would be neigh impossible, so having a different process load compared to the baseline is also a no go. Your suggestion to try showing a net energy savings from "natural ventilation", is a valid path, but it is probably more likely to show an enery wasting than an energy saving (this is the very reason why it is steared away from in all but the most ideal climates). Even properly designed natural systems have a hard time meeting both comfort and energy saving criteria. If this is a new construction, you should talk to the architect about standard 90.1 and don't forget about the vestibule requirements. Perhaps, they can make it a properly enclosed area.