The current Apple Store would be hard to rehab into something else, and Apple wouldn't like some other company reaping the benefits of their proprietary glass work. I wouldn't be surprise if they knock it down themselves once they move.
The Pioneer Court news is great to me. It won't take up very much room at the surface level, they have entrance designs much more compact than the 5th Ave cube. Plus, moving the retail nexus further south is very exciting given all the new work going on south of the river.
Edit: also, regarding Pioneer Court, they whore that thing out for branded marketing shit all the time. Every time I go through it I have to bob and weave through people handing out free samples of candy and stages set up for livestreamed concerts sponsored by Dodge Edge Shaving Gel Banana Republic Minions Now In Theaters. I don't think there's much integrity to preserve there, and as streetline points out above, they can do very compact entrance structures. I'd bet they might have it located very close to the water's edge, and the "underground" store might have an open window overlooking the river.