I think it would be unusual for a signaller to re-route a freight train that was booked via Stratford onto the GOBLIN or vice versa, without the route control and freight operator being involved and a specific reason for doing it, such as route knowledge or infrastructure faults as mentioned in the initial post. In this case I suspect it was more to do with the potential for delay when routed through Stratford, as noted by Freightmaster.
Looking at freight trains running between Barking and Stratford between 06:00 and 22:00 on Monday 7th, the majority of trains running this way are doing so to access the Canonbury curve onto the ECML (4E24 London Gateway - Leeds, 4E07 London Gateway - Doncaster Railport, 4E39 Tilbury LCT - Wakefield, 4E97 London Gateway - Rotherham). With the exception of 4M03, it's not until 4S60 21:15 London Gateway - Coatbridge that a freight train runs from Barking via Stratford to Gospel Oak (and that doesn't pass through Stratford until after 22:00).
4M03 on Monday 7th was 10 minutes late through Woodgrange Park - a quick look at trains on the main line between Stratford and Shenfield around this time reveals that in the eastbound direction it delayed 1P40 by 3 minutes, 1N28 by 3 minutes, and 2K60 by 3 minutes. In the westbound direction it delayed 1K75, 9Y47, 1N41 all by 4 minutes each. These are not huge delays, but passing through Stratford at 15:21 on a weekday, those sort of delays can ripple out into the evening peak and cause further delays to be attributed to 4M03, especially with Crossrail trains added to the mix.
It's possible that it was agreed between Network Rail and Freightliner that it would be better to re-route the train via South Tottenham for the rest of the week, "under control arrangements" without new schedules being created. Unless everything is running on time through Stratford, it must be a headache to signal freight trains through there to and from Barking during the day.
Then why is it pathed via Stratford if they’re never going to run it that way?
That would be the next logical question! As noted, 4M03 was running on STP schedules all week, so it's not an established WTT path. On the days it ran via South Tottenham, there were delays to 2J74 (14:48 Barking Riverside to Gospel Oak) on the 8th and 11th, but on the 9th and 10th it looks like it was possible to have 4M03 be on time through Tilbury Town, give it a clear run through Barking and be over 10 minutes early at Woodgrange Park, allowing it to get ahead of 2J74 without delaying it (which I guess is the sort of "margin that isn't compliant in the timetable" mentioned by The Planner).
In summary... I suspect that on paper the path via South Tottenham didn't work and the one via Stratford did, but in reality sending it via Stratford revealed an undesirable performance risk that they preferred to avoid by sending it via the GOBLIN for the rest of the week.
