To answer your question, you got charged the standard NR fare via Zone 1 as you used London Terminals.

It would've been cheaper to travel to Clapham Junction from HOP, then go to Mortlake that way. You'd still be charged the NR rate too.

On the way back, you'd got charged the combined TfL/NR rate which is the standard NR fare to Waterloo plus £1.10 as you used both NR and TfL services.

The principle is from now on, if you use the Overground and don't travel via London Bridge to get into town, you'll get charged the TfL fare. If you use London Bridge or other stations in the national rail network, such as East Croydon, Purley or Sutton, the old National Rail Oyster PAYG fare still applies.