For reference, Page 2-4 (pdf page 19)
has the Seneca Yard and surrounding "sub" yards.
Yes, If BPRR were to start using one of the old South Buffalo yards, yes they'd still have to foul into either the main yard and back down into the old "H" yard, or make their way all the way up "17" across "The Shenandoah" and then back into the "PS" Yard.
My point is, though, that anything involving the Seneca Yard and vicinity would only work if they were to increase their interchanging with CSX and (probably) drastically reduce their interchanging with NS, which could be awkward considering they're leasing said Buffalo Line from NS. I would guess this is why NS stopped using that section of the Buffalo Line to begin with - it comes out in a really inconvenient spot for anyone who doesn't already own the yard and main lines down there, which is why it worked for Conrail. Continuing to access the Buff Crk Yard while avoiding CP Draw would involve one of the other options I listed above, most likely.