The simple answer is yes! cove.tool is part of getting the deduction since a design team needs to figure out which reduction would allow you to achieve the percentage reduction for each qualifying category. It is much easier to do this in the early stage of the project when you can run hundreds of models using machine learning to reduce the cost and maximize the energy savings. See here for how to run an optimization in cove.tool. We use the EnergyPlus/OpenStudio integration and this is the best and most acceptable energy model for the tax deduction.
Below is a summary of the areas you can work on to maximize the tax credit. Play with these categories in the optimization.
For more information from the US Department of Energy see here: https://www.energy.gov/eere/buildings/179d-commercial-buildings-energy-efficiency-tax-deduction