We faced similar questions for a project that got certified under NC, but in your case CI may make the most sense.

We had several communications with the USGBC (this was pre-GBCI) to determine what rating system would apply. We settled on NC as the renovations to an existing industrial building and its systems were extensive enough to qualify as a major renovation.

In our case, the LEED boundary included the whole building and site. Although the scope of work that was tracked for MR and EQc4 credits was limited to the renovation work, we still had to account for the whole site performance for stormwater, parking, heat island, and light pollution credits, and the whole building performance for water, energy, lighting, and ventilation, including process loads.

If you are pursuing CI, and the office and industrial area is to be occupied by the same tenant, you may need to include the whole building, not just the office, in the LEED boundary. This could mean having to account for accounting for the lighting power density, ventilation rates, and HVAC performance in those areas, but I imagine you might be able to exclude process loads.

Your situation is not an easy one to fit into LEED, since the extent of the work the owner is doing may not be extensive enough to qualify them as a "green building." I've heard that the USGBC is working on adapting the rating systems to fit unique building types such as data centers, hospitals, and also warehouses, so it would be good to contact them directly and verify if CI would apply.