Our of interest, what is the problem with sending electrically-hauled freight through Waverley in the small hours?
Edinburgh used to have two through lines and was a lot quieter at night.
Now, with quite an intensive timetable, earlier and later trains, with a lot stabling in Waverley overnight, and with the sleeper taking up two through platforms for several hours at a time, the station is quite full overnight. Some of the station overnight is used for track inspections or work, and there's usually a blockage overnight somewhere in the central belt.
There's also issues with electric haulage. Most electric hauled trains tend to go west coast, whereas most east coast trains travel off wires for quite a distance. No use using an electric loco if you'd have to change halfway, and if it's diesel hauled you may as well send it around the sub.
Millerhill isn't as big a traffic producer as it used to be, so less freight in general coming up the ECML.
There are also gauge issues in the tunnels either side of Waverley for large containers, which don't exist if you send them around the sub.
In all, it's just easier to use diesel and send it the back way, keeps it out the way and you don't have to worry about any if these.