For electrification, you would need a dual standard --
one height of wire for lines without double-stack
container traffic and one for those with. There is
available technology for having pantographs that can
operate at multiple wire heights, which I won't go
into here.

There are a number of ways of dealing with clearance
issues. Two that have been used in Europe are:

Under a relatively short bridge which imposes clearance
issues, simply put in a short segment of non-energized
wire. Trains coast through. There are lineside signs
that instruct the engineer to pull the main breaker and
to close it again after exiting the non-energized segment.
This can also be done automatically with wayside
transponders, if engines are appropriately equipped.

In some tunnels with close clearances, rather than re-
working the tunnel, railroads have replaced the full
catenary suspension of the overhead wire with an overhead
rail. Yes, the pantograph tracks along a fixed metal
rail, though smaller than the rails that the trains ride
on. Mounting such a rail to the tunnel ceiling (or
underside of a bridge) with appropriate insulators takes
up less space than the catenary, whose supports have to
be mounted into the side of the tunnel. Yes, there is
a way to deal with having this rail in segments. You just
overlap the ends with each end bent slightly upwards.

-- Ernest