Energy Modeling In a High bay Industrial area + Office

Option 2 would not apply to your situation. You cannot use it and get the whole building certified. You would need to follow Option 1. The proposed case is always modeled as designed and the baseline according to Appendix G. Since the manufacturing area is unconditioned you model it that way in both models. Any manufacturing process loads or ventilation fans in this area is modeled identically in both models. Since the office is the only conditioned space you use that area to enter Table G3.1.1A and select the baseline HVAC system. In general you cannot use the energy model to demonstrate ASHRAE 62.1 compliance. The calculations you do for IEQp1 however, should be consistent with the models.

Will it be ventilated with any fans or strictly by passive means?

How to handle if there are absolutely no conditioned spaces in a manufacturing facility or probably an unconditioned office building? Is it accepted if we just show compliance with only lighting and equipment loads.

Marcelo - See the Case 2 compliance paths under IEQc2. Any of those natural ventilation options can be used to demonstrate compliance for IEQp1. An airflow model is one of the options.

Rathnashree - if the entire building is unconditioned then it gets modeled identically for HVAC. You can claim lighting and equipment savings. You must show compliance with the ventilation requirements for IEQp1.