They can with special permission from the FRA. NJT does it with the RiverLINE in South Jersey, and it will be done with the Northern Branch. A small section of the Newark Light Rail had freight on it until 2007. The NS Newark Branch sees very little traffic, so I doubt NJT will have any issues using the line. The height of the Catenary can be adjusted for freight clearance its not a fixed height. SEPTA has a section of streetcar that crosses the CSX main line and catenary is higher to meet the clearence of the double stack.