Since the Decision to approve the project--issued Sept. 8, 2016--has a 3-year expiration date, and given the timing of these latest permits so close to the 3-year deadline, sounds like the developer is just trying to keep the project alive so that they don't have to seek a new land use review.
From the
Approval:
Expiration of this approval. An approval expires three years from the date the final decision is rendered unless a building permit has been issued, or the approved activity has begun. Where a site has received approval for multiple developments, and a building permit is not issued for all of the approved development within three years of the date of the final decision, a new land use review will be required before a permit will be issued for the remaining development, subject to the Zoning Code in effect at that time.