"The problem is the AI deems that going in reverse is quicker"
It will if the direct route is blocked. Allways been a problem with Ai's taking short or long cuts.
The track direction markers should stop the Ai reversing, in driver note where the rear of the consist is, then in surveyor place a direction marker or 2 down about 100 metres to the rear of that.
Another way is use command drive to track mark xxx (before container station) then use command wait for trigger xxxx (placed at exit of container station) to be triggered by any train. The consist will then wait for the train in front to start exiting container station before entering itself.
Only snag is if there isn't one exiting there it'll sit all day, solution is drag the trigger command out if not needed.
Final idea but the hardest is redo the track into the container station, you need enough track to take your longest consist, then container station, then enough track again plus a few hundred metres before the first set of points (so consist doesn't derail while loading).