I don't get why that would be allowed to happen.
Isn't the government's angle to buy piecemeal spectrum from broadcasters and then auction huge nationwide blocks at a significant profit?
Not exactly certain what you're asking, but I think you may be conflating the auction and the repacking. Once the forward auction is completed and the new spectrum channel plan public notice is published, the 39 month repacking begins. (Whether or not 39 months is sufficient time is another hotly contested point.) If however, in a given market an uplink/downlink channel pair is already unoccupied, the new licensee(s) can begin operations (testing really) immediately; they do not have to wait the until the absolute end of the repack time period. This is to what the article refers, in a rather poor manner for those with more than a mere passing interest.
Again, as of right now, in major urban markets, be prepared for LTE testing to begin, and thus interference, as early as summer 2017.