I'm not real sure that the LIRR actually stores any of the few diesel hauled multi-level sets in the Hudson Yards. I typically see them being deadheaded in & out when I'm at Woodside.
That said, since the Hudson Yards project is just barely getting started, I can't imagine that the LIRR and MTA would have allowed any design for the table that they'll build upon to prevent running multi-levels into the yard. If the overhead project had come before the yard, things might have been different. But to allow construction of something new to limit options would be unthinkable and silly.