2M50 should never have passed L253. For me, that was the most significant decision.
Agreed in reality if 2M50 had not passed L253 then once it became clear that 2M48 wasn't clearing the section anytime soon then 2M50 could have been sent into an alternative platform and terminated and kept the junction clear for other trains to pass. Though I can certainly see why the signaller did what they did! A busy day with lots of disruption which causes pressure/distraction and so you fall back on the habit of authorising trains to follow closely behind each other rather than taking that step back to think "hang on, 2M48 is having difficulty departing so I'll just hang-fire a minute and hold it at L253 rather than L445 to keep my options open".
One thing that struck me, and I don't think it's mentioned by the RAIB report, is the role that perhaps fatigue and break arrangements played on the signaller at this point? According to the report shifts at London Bridge were 12 hours long with shift change at roughly 0645 and 1845 so by the time this is all kicking off from 1730 onwards the signaller has been on duty for around 11 hours. Plus we are told that they returned to the panel at 1730 having been on an hours break (so presumably between around 1630 to 1730). I do wonder if the impact of being on duty for 11 hours and just coming back from a break so still getting "back in the saddle" so to speak perhaps played a role?