In principle I don't disagree - Oyster fares have always been charged based on the route taken - but practicalities dictate that it often isn't possible to conclusively detect double-backs and so the benefit of the doubt must be given.
No, Oyster (and hence contactless PAYG) fares have always been based on the ASSUMED (rather than actual) route taken - sometimes, by pink reader touch or (enforced) OSI (or not) a selection between assumable routes is possible (and specified) - but not always. (There is a note in the TfL Single fares finder "Some journeys are charged via Zone 1 irrespective of the route taken")
Saying that such fares are 'zonal' (based on zones traversed) is somewhat misleading: they are station to station fares, though determined by start and finish zone, and assumed zones traversed (which assumption may or may not be accurate).
When you bear in mind that Oyster was originally an LU concept where TfL are quite happy for passengers to travel from zone 1 to Neasden (3) via Wembley Park (4), it's obviously a conscious design decision. In practice I'd say that most TOCs are happy for people to circulate if they can be sure that they won't try to exit at the further point for a cheaper fare. PAYG solves that issue because if you do exit at Shenfield then you're charged the correct fare.
I would say that it's intrinsic to the whole PAYG concept: when you start your journey by touching in, you are effectively contracting/agreeing to pay for a journey from your departure station to some other station, by some route, when you end your journey the fare (from start to end, by assumed route) is looked up, and charged, as if by magic. Beyond the (limited) cases of pink reader or via OSI alternative assumed routes the route to be or actually taken is neither specified, nor (without great difficulty/cost) determinable, so it has just be assumed - the system just knows starting and end stations, and so has to charge the appropriate station to station fare.
The PAYG paradigm is that a journey is from one station to another, with fares being based on this concept, with route being largely irrelevant.