Low Speed High Volume Fans - Penalty in model for using?

What function do the fans serve? Are they exhaust fans, ventilation fans, ceiling fans?

Such fans are not regulated by 90.1 so they are considered a process load. As such they should be modeled identically in both models. So no penalty but no savings either. If you wish to claim savings then you must follow the exceptional calculation method. Be sure to firmly establish the baseline for any savings you are claiming. The baseline should be based on typical industry proactice in your area. So if ceiling fans are not typically installed in such facilities you will need to document that. Maybe big ass fans can help you with the documentation. In my experience ceiling fans can be an energy saver is spaces that are cooled. The movement of air will have a cooling effect and allows temperature setting to be a bit higher for the same level of comfort. On the heating side they generally do not save energy. You will typically need at least a 20 degree temperature differential to overcome the air movement effect and that level of temperature stratification rarely exists in high ceiling facilities in my expereince measuring ceiling temperature in hundreds of facilities. Slow air movement can help a bit but again you need significant temperature stratification.