Two thoughts come to mind:
1 Are the actual container weights used or is an average used? In other words, would it make a difference if all of the containers were loaded with baked beans rather than a mix of baked beans and paper tissues?
2 The train weight was established some years ago before the review of coupler strength enabled extra wagons being added to the train. Was the train load reviewed as well?
The actual container weights are provided by the terminal to the train operator, and these are entered into TOPS.
The TOPS system adds the weight of the containers on each wagon to the wagon tare weight and checks each wagon is not overloaded. This is highly unlikely with the usual 45ft containers on 4S43 - if they are a legal weight for road haulage they should be fine on a train - but is possible for example when loading heavily laden 20ft containers (which can weigh more than 30 tons each) to wagons which can carry three of them.
The TOPS system then adds the gross weights of the wagons on the train together, and checks this does not exceed the maximum weight for the loco type on that route. This is most likely limited by the 1400 tons trailing weight given in the "loads book" for a single class 88 northbound over Shap and Beattock, rather than a coupling strength restriction. A pair of class 90s or a 66 will typically have a timing load of 1600 tons for an intermodal train on the same route, although northbound Freightliner services between Basford Hall and Coatbridge are usually lighter than the domestic intermodal services running north from Daventry.
The total train weight on 4S43 (or any other intermodal) can vary from day to day depending on the precise mix of containers and their contents, yes. If 4S43 had all containers stuffed full of pallets of baked beans it could end up being too heavy for the loco to pull and needing to have wagons detached, but this should be taken into account when they are planning which containers to load to each train.
Some trailing weights (i.e. not including loco) noted on 4S43 on a few random dates over the last year or so have been 1236, 1244, 1249 tons. When 4S43 failed on 17th December it had 20 wagons weighing 1334 tons behind a single 88. I think 20 twin wagons (IKA and IDA) is usually the maximum length, but it often runs with slightly fewer wagons than that. From the small sample of old consists I've seen, the highest load I noted for a single 88 was 1371 tons in July last year, quite close to the 1400 ton limit.
I cannot understand why one of the Tilbury to Daventry trains (4M07/4L27) uses a class 66 when it seems to be perfect for an 88?
Now that you mention it, 88003 ran light from Gresty Bridge to Daventry on Monday as 0K44 and has been working the 4L48 to Tilbury and 4M77 return every day since then.
As per above post, I suspect the normal use of 66s is based around the loco diagrams - for example 66424 worked 4M77 on 8th July followed by 4V44 to Wentloog. I'm not sure how these diagrams usually work; some of the Wentloog trains are being retimed and diverted at the moment (via Bletchley, Oxford, Swindon and Bath Spa) which may have altered the usual diagrams this week and resulted in an 88 being dedicated to the Tilbury service.