Railroads generally prefer undercutting (lowering the roadbed) over bridge-rebuilding when needing to obtain higher clearances. This is less expensive and requires less coordination with local municipalities.
There is no inherent conflict between double-stacks and wires, so long as the wire is strung above double-stack clearance. (This may require further undercutting, whenever feasible.) As an example, NS trains accessing the Trenton Cutoff have to clear under catenary at either end of the cutoff: to access the former Reading main line in Norristown, they must run through a station used by SEPTA's (electrified) commuter rail services; conversely, the connection on the eastern end is to the NEC--also under wire. These trains do not leave this alignment for some time--I believe Oak Point Yard (Port of Newark) would be their destination.
Remember that in the last couple of decades our railroads have invested considerably in creating double-stack-capable trunk mains; this has required rebuilding tunnels, undercutting at bridges, etc.; there's no reason our railroads can't use the same techniques to wire those same lines.
"A train or a train concept with a history of success elsewhere should by default be legal on mainline tracks in the US and so should the established operating and maintenance practice..." --
Alon Levy