Given that USGBC Reduced Occupancy Guidance document explicitly states that its guidance for EAp2/EAc1 is identical to the Energy Star guidance, seems safe to assume that a) USGBC fully intended to mirror Energy Star, and b) Energy Star subsequently changed its guidance.
If I were you, I would follow the current Portfolio Manager guidance. If you are very worried that it won't be accepted for LEED (seems unlikely), you can always try your hand with GBCI customer service.