If I was a council person, I would like to have current and independent appraisals of Interline and each Riverfront Parcel before making any kind of land swap. Take all of the entities involved and their prospective plans to improve Downtown out of the equation and imagine that COJ was making a land swap elsewhere Downtown without having a current appraisal of the properties involved.
That said, this is a unique situation and there seems to be a fairly simple solution to the deal that protects all parties. In UF's land swap with COJ, they have to complete construction on parcel A and start construction on Parcel B before commencing any work on the Prime Osborn. COJ could structure the Riverfront parcels/Interline land swap similarly, but instead tie it to the development of Gateway Jax. Gateway appears to be getting a favorable deal here to open the door for UF, but presumably also because of their other plans downtown. So give Gateway one of the parcels directly for the Interline Building and allow them to have the other parcel for free once they have hit certain benchmarks for Gateway (similar to the Prime Osborn deal). As a very small carrot/olive branch to Gateway for this deal, it would keep them from paying property taxes on one of the Riverfront parcels for a period of time.
As with the revised Laura Street Trio deal, there are probably 20 different ways to structure a deal that protects all the parties and ensures benchmarks are met.