Portfolio Manager uses the total energy consumed, including both traditional and green (on-site and off-site green power) sources, when calculating the energy intensity a property (i.e. EUI metrics).
Portfolio Manager doesn't benchmark buildings using net zero energy consumption as a target. Instead, the ultimate goal of the tool is to benchmark how energy efficient your property is based on how intensive the total energy usage is per square foot, with some adjustments for use details (number of workers and computers). It's possible for a building to reach net zero energy consumption yet actually be less efficient in terms of how intensely energy is consumed on-site when compared to another property.
That being said, green power is more efficient at the source and that does affect some metrics and can improve how a property scores. You can read more about how green power is incorporated into those calculations in this FAQ for on-site green power and this FAQ for off-site green power.
See the related article: Do I receive "credit" in my score for the onsite green power that I export back to the grid?