But I could change at Stratford to the Central line to Liverpool Street and not have to tap out to get the Lizzie line and therefore be charged the lesser fare.......
Secondly when phase 2 opens I could change at Liverpool Street without tapping out and be charged the lesser fare too
Well yes, the default route assumes travel avoiding Zone 1. So if you don't touch out and in at any intermediate Zone 1 barriers, you won't be charged the Zone 1 premium. But you can hardly complain if you are charged the via Zone 1 fare for travelling via Zone 1! You can't have your cake and eat it.
I would imagine that they have some scope to make STP amendments to the movements at the Plumstead end. Paddington obviously might be a little more difficult as it has to interact with the relief line timetable.
I imagine they could even run the first few trains empty each day, although that seems a little pointless.
Of course - and services will need to be STP'd (or the LTP schedules split) to make them advertised. But as this timetable is what has been running during Trial Operations I would be surprised if the public timetable were different. I suppose there could be some slight changes to allow for longer engineering/testing access hours.
Also showing Heathrow as zone 6 is highly disengous given the premium fare.
There are multiple fare scales in operation across different modes, so the notion that the cost of Zone 1-6 trip may vary is hardly novel. I think it would be more unhelpful to say that special fares apply, as that might lead anyone who holds a Travelcard or is reliant upon capping to think that it's like the Heathrow/Gatwick Express or HS1 and carries its own uncapped standalone fare.
But either way this is unaffected by the opening of the Core section.
Technically you shouldn’t enter zone 1 if you are not buying zone 1 fare.
If travelling on Oyster/contactless, you can take whichever route you like; the system will automatically charge you the correct amount.