How to document a non-LEED-certifiable building?

The 90.1 definition of unconditioned space is not accurate. The parameters you indicate define fully conditioned space. Semiheated spaces >3.4BTU/h.sf are still considered "conditioned" spaces. Anything that is not fully conditioned or semiheated is considered unconditioned. I would guess your spaces are semiheated and should follow the 90.1 requirements as such.

1. Yes it should be included in the model. I would just include it in the same model and the larger building. It would probably be a good idea to model this building on separate meters within the model. You could model it in a separate model and add them together as well.

2. Yes any conditioned or semiheated space should be included in all credits for consistency. Unconditioned parking is not included in the GFA but should be noted. The reviewer will be expecting the GFA reported for the model to be within 10% of the total GFA.

3. Yes you need to account for all energy use within and associated with the project. If this load is outside conditioned spaces you could do the calculations outside the modeling software and simply add the results to the modeling results. If it is within conditioned space then you will need to add this load within the model as well.

How do you treat naturally ventilated, occupied, interior space with no mechanical heating or cooling? Do you count it as conditioned or unconditioned? Do you include its area in the Gross Floor Area?

It is unconditioned space by definition. The most common occurrence we see would be in a warehouse. Since it is regularly occupied space it counts toward the GFA for LEED.

Here in Climate Zone 5, few spaces besides warehouses are likely to use natural ventilation without mechanical heating or cooling. In some other climates, might many other space types fall into this category?

In such cases, there could be more than 10% difference between the energy model GFA and the project’s total GFA.

Would naturally ventilated spaces that use passive heating and cooling strategies also qualify as unconditioned?

Some climates can get away with it but the prevalence I see is more cultural. Many international projects in warm or mild climates use natural ventilation for occupied spaces. I have seen many international projects submitted for LEED from many different space types that do not have heating or cooling systems. Not so much in the US.

There could be more than a 10% difference. If there is it should be explained. In an unconditioned warehouse you still have lighting, ventilation, and other equipment loads. These need to be modeled but because they do not necessarily have interactive effects with other energy end uses, they do not necessarily need to be modeled in a space depending on the strategies employed.

If naturally ventilated spaces do not have installed heating or cooling then they are considered unconditioned.

I have also seen questions about how to treat mechanical chases, airshafts, and atria.

As I understand it, mechanical chases that are inside the building enclosure count toward Gross Floor Area (but not net area). Since they are inside the weather barrier, IEQc4 Indoor Air Quality restrictions would apply, but I am not sure how to treat chases in energy models. Would these be unconditioned space—part of that 10% gap between Project GFA and Conditioned GFA?

By contrast, airshafts and light wells are generally open to the sky, so they are exterior space. They do not figure into GFA or the IEQc4 credits.

Finally, in an interior, multistory space like an atrium, the floor area only counts once in the GFA and in the model. Thus, you would model a three-story lobby as one very tall room, not as three spaces stacked on top of one another. (I worked with a newbie modeler who inadvertently did the latter. This effectively tripled the square-footage and the energy load of the atrium and doubled the Building GFA. That was a bit more than 10%.)

Does this just about cover the ins-and-outs of reconciling energy models with Project GFA?

Most chases are like interior partitions. They would be part of the difference between gross and net.

One potential issue with chases is that some can have a relatively significant impact on energy use. Elevators in a high rise building come to mind. They basically are large interior chimneys that can have a major impact on air movement in and out of the building, especially if they are vented at the top. In certain situations I think that they should be modeled since they will impact energy use.

The most important thing is to make sure your model accurately reflects all of the items which will impact energy use. If you look at these issues in that light you will always understand what is the right thing to do.