I know that the Highway Code says you can enter a box junction if turning right and the only impediment is the oncoming traffic.
At troublesome junctions there is often a filter to allow time for probably 2-3 cars or one artic to get round. If you are turning right with a car in front of you, probably best to stay right back and wait for the change of traffic lights because the likely scenario is that one or two of the cars coming the opposite way come through on an amber/red and the filter time is further reduced.
In the circumstance you describe, perhaps if you had pulled forward into the box junction you would have still been blocking the crossing due to the length of your vehicle. At the end of the day, when you crossed the line the lights were green and you are allowed to pull forward if turning right.
It didn’t warrant a driving fault, so happy days.