Hey!
Are you trying to add the fabric to your NDI at initial site setup or do you have issues with data collection after that?
During initial adding of your site in NDI I would go with adding the physical APIC using it's OOB IP (add one if you don't have one already).
I don't think it is a must-have for NDI to reach your virtual APICs, as long as the OOB connectivity to the physical APIC is good.
In-Band reachability of all Switches is more important
BR Jules