Maybe I'm mistaken about the path the LSL takes. Does it go through the wye which is just east of the Exchange Street station?
Yes. The problem is not the move on the Wye to Exchange Street. The problem is the Wye itself. It basically carries a huge mount of CSX freight traffic on its south-east leg. A backup move there would be into that flow of traffic closing down one or both tracks for a while, which would be unacceptable.
Even if BCT were ever revived, what would make most sense is to go with a track layout similar to the one being built at Rochester, since it minimizes conflicts. Of course, that would mean a very long walk from the terminal building to the platform, which would be between the two main line tracks of CSX.
Depew really should be fixed similarly. It causes a lot of headache for everyone and delays all around because (a) it involves conflicting moves tog et to the single track platform off to the side, and (b) if two trains land up there at about the same time, one has to wait blocking one of the main line tracks while the other finishes its station work. As more trains are added west of Albany, this will become an increasing problem.