You’ve stumbled upon a mistake in the fare database. The £5.50 fare is supposed to be avoiding zone 1. This can be done by taking the Overground to Surrey Quays and then heading back towards West Croydon. Because it’s the default fare it is charged if no other touches are made, and no touches are required at London Bridge as long as you stay within the paid area. Obviously when starting at New Cross Gate you won’t enter zone 1 so the fare from there is correct.
And yes, any travel after 0930 is counted towards the off-peak cap, even between 1600-1900, and with a railcard the cap is reduced.