In COMcheck 4.0.0.3 and newer, you can now break up your VRF into two systems. One can be defined as the VRF Outdoor/Central unit and is selected as heating equipment→heat pump list-→"VRF xxxx". This type of system will enforce the system efficiency depending on the system cooling capacity.
If the economizer requirement is enforced you can select the economizer exception "VRF Outdoor/Central Unit". The other VRF system you would specify is from the cooling equipment side of the HVAC systems dialog and is called "VRF Zone Fan Unit". If you select this as your system the capacity of individual units will generally be so small that the economizer requirement will not be enforced. And the system efficiency is also not enforced as there is no efficiency requirement for this part of the VRF system.
Notes: If you don't find the VRF system available in the HVAC system dialog then it is probably due to the energy code you have selected. Some energy codes don't enforce compliance with VRF systems. 2009 IECC and 90.1-2007 are 2 of them. If VRF isn't found in the energy code being used it is because it is not enforced by that energy code.