I sort of get it though. Conley relies pretty much exclusively on the Butler Freight corridor bridge that runs on the waterfront side of the site. If I were Massport, I'd also not want to have to field resident complaints about rumbling clangy container trucks under windows and balconies. There's a reason Butler is carefully avoided in almost every render I've ever seen of this, but that "waterfront promenade" is still going to be looking at it and the thousands of trucks that use it. Plus, the other side immediately overlooks the container port. Those are loud, industrial uses - I don't blame Massport for wanting to prevent the possibility of complaints.
Here, it gave Massport leverage to push the residential away from the waterfront which isn't what you would normally want. Look at airports, race tracks, and other loud uses. "It was here first" doesn't stop people buying homes near some loud preexisting facility then campaigning to get it shut down.
