NY&A Operations per East New York Tunnel

Put this here, since LIRR owns the rail corridor.
Anyone know the current relevance of the lowered track through the active tunnel? I've read that the lowering was tied to the use of specially designed cars, for carrying intermodal containers through the relatively low underpasses on Long Island. But, that the effort was abandoned after bogie related derailment problems.
Ergo, is there any current purpose for using the higher clearance tunnel over the others?
I ask this, because the MTA's PEL report prospectus on the IBX (which isn't really 'X'; another marketing ploy) has the freight track moving one tunnel over. The report covers many construction needs, including that of rehabilitating the tunnels chosen, for passenger rail, to be compliant with federal regulations, but yet there is no mention at all about making the 'new' (2/3 mile) freight tunnel fit the dimensions of the current freight tunnel.
The PEL report covers the history of the tunnels, including the track lowering in the one, but doesn't make note of the clearance need no longer being relevant.
Any inside scoops on this?

The track was undercut in the tunnel to handle Plate F railcars. If freight traffic were to be moved to the other tunnel that still has rail, that track would have to be undercut to the same specs.

Yes, I now see their page on the parent company website makes note of the Plate F clearances, so makes sense that they would want to maintain that capability.
Had only seen the original use which prompted the track lowering, with that use often noted as no longer a need.
Thanks for clearing that up.