I'm guessing that they won't go with the option to fill the southwest lower portion of the yard given the expense and inability to continue ops. during construction. Instead, I think they'll extend the un/loading pull-through tracks, TV-1 and 2, eastward to/toward CP-43. They should be able to get at least the lower specs. of 90' between track centers to support a packer operation between 2 un/loading tracks for a good deal of the way or without too much embankment excavation. However, this will require the removal of Leroy's Junkyard (he or his offspring will be happily counting their money somewhere else no doubt!), loss of track capacity to support Delaware Express (off to Westborough, E Brookfield or the G&U?) and ~1500' of lower yard un/loading track capy., probably 2 "short term" flatcar storage tracks in the yard (maybe not?), and, a couple of smaller tracks ('engine house" and "34 extension"). But, this would also facilitate parking expansion and/or the necessary "ramp" to bridge Franklin St.
I'm thinking the extension eastward to Fantasia St. involves the TV yard lead track to give some head-room for eastbounds or their power when spotting their trains or for switching from the east end without going out onto main Tk #2 at CP-43 (though not necessarily long enough to completely eliminate the need to enter the main at CP-43 for working the east end of the yard). Perhaps that extension would also serve to provide a place, east of Putnam Lane, for laying power over in the parcel occupied by the defunct golf driving range?
They may be able to hedge with flatcar storage for the time being because there will be fewer flatcars needed with the conversion of today's single-stack domestic container operation to doublestack. If they do have to add storage capacity, I'd guess it would be done with an extension of the third track west of CP-45. Those baretable moves to Beacon Park are generally part of the overall flatcar storage tactics for the weekly weekend inbound flatcar accumulation cycle with westbound re-loading occuring during the week once containers are delivered to customers and returned.
As Mr. Tosh notes, it'll be interesting to see how this pans out. And, I'm curious if CSX will shift their international doublestack business from the P&W over to E. Worcester once this project is complete.