John,
Thank you very much for this information. I’ll try and answer your questions as best I can.
1) Unless they have changed things then yes, the first touch in on a journey sets the rate for the whole journey.
2) Yes, if you pass through zone 1 and out the other side then a peak fare is payable, unless you’ve come from GWR stations from Iver westwards (including the branchlines) where it’s off-peak for any eastbound journey in the afternoon.
3) The fare-finder does specify whether the fare will be peak or off-peak in the afternoon. The times against the peak fare change depending on whether it is am only, am and pm, or pm only.
4) Correct, the off-peak cap applies at any time after 0930 and limits the effect of peak evening fares if earlier travel was off-peak after 0930. The anytime (or peak) cap protects revenue when the inbound journey is before 0930.
Do come back to me if you get any further questions.