It seems likely they'll do the bare minimum to accommodate paper tickets on the route - single fares between the core stations only, everyone else having to use Oyster/contactless or having a cross-London or Zone U12 ticket.
As the PAYG fare scale will be "Tube", it will cost the same to use as the Tube does. That means, for 99% of people travelling from within the numbered Zones, the PAYG fare will be the same to Paddington LL or Liverpool Street LL as it is for any other "core" station.
However for those travelling on a journey which involves non-Tube fare scales, e.g. Shenfield or Reading-Langley (inclusive), or connecting from Southeastern into Abbey Wood, they will be charged a Zone 1 'Tube single' on top. Again, no different to the Tube.
Basically for ticketing purposes it will be another Tube line.
a Richmond-Upminster journey could be done direct (and slow) by District line, or could take overground via North London line and Gospel Oak Barking, or could change via Ealing Broadway then Crossrail to Romford, or even Waterloo then jubilee to West Ham. Are they all valid routes ?
I'm not sure about the Ealing Broadway route but on a paper ticket those would probably all be valid. Thing is, it'd have to be a very unusual set of circumstances to warrant buying a paper single or return, given how much cheaper the PAYG fares are.
But suppose you started further out, say Staines and went on to Southend, does that then become a cross London journey with non zonal fares, and can you still use the crossrail route within the above combinations.
Yes, it would be treated exactly the same as Thameslink or the Tube. It's simply a cross London transfer.